Journal of Microbiology

Volume 58(12); December 2020

Review

[MINIREVIEW]Regulation of gene expression by protein lysine acetylation in Salmonella: Hyojeong Koo , Shinae Park , Min-Kyu Kwak , Jung-Shin Lee; J. Microbiol. 2020;58(12):979-987. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-020-0483-8

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Abstract: Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNAbinding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.

Journal Articles

Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina: Kah-Ooi Chua , Wah-Seng See-Too , Jia-Yi Tan , Sze-Looi Song , Hoi-Sen Yong , Wai-Fong Yin , Kok-Gan Chan; J. Microbiol. 2020;58(12):988-997. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0325-8

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7 Citations

Abstract: In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1 ω7c, C16:0, C19:0 ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteraceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

Patterns and drivers of Vibrio isolates phylogenetic diversity in the Beibu Gulf, China: Xing Chen , Hong Du , Si Chen , Xiaoli Li , Huaxian Zhao , Qiangsheng Xu , Jinli Tang , Gonglingxia Jiang , Shuqi Zou , Ke Dong , Jonathan M. Adams , Nan Li , Chengjian Jiang; J. Microbiol. 2020;58(12):998-1009. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0293-z

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Abstract: Members of the genus Vibrio are ubiquitous in aquatic environments and can be found either in a culturable or a viable but nonculturable (VBNC) state. Despite widespread concerns as to how to define the occurrence and dynamics of Vibrio populations by culture-independent approaches, further physiological research and relevant biotechnological developments will require the isolation and cultivation of the microbes from various environments. The present work provides data and perspectives on our understanding of culturable Vibrio community structure and diversity in the Beibu Gulf. Finally, we isolated 1,037 strains of Vibrio from 45 samples and identified 18 different species. Vibrio alginolyticus, V. cyclitrophicus, V. tasmaniensis, V. brasiliensis, and V. splendidus were the dominant species that had regional distribution characteristics. The correlation between the quantitative distribution and community structure of culturable Vibrio and environmental factors varied with the Vibrio species and geographical locations. Among them, salinity, nitrogen, and phosphorus were the main factors affecting the diversity of culturable Vibrio. These results help to fill a knowledge gap on Vibrio diversity and provide data for predicting and controlling pathogenic Vibrio outbreaks in the Beibu Gulf.

Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil: Dockyu Kim , Namyi Chae , Mincheol Kim , Sungjin Nam , Eungbin Kim , Hyoungseok Lee; J. Microbiol. 2020;58(12):1010-1017. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0490-9

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Abstract: Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica: Mincheol Kim , Hyunjun Cho , Won Young Lee; J. Microbiol. 2020;58(12):1018-1026. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0524-3

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10 Citations

Abstract: The gut microbiome provides ecological information about host animals, but we still have limited knowledge of the gut microbiome, particularly for animals inhabiting remote locations, such as Antarctica. Here, we compared fecal microbiota between southern elephant seals (Mirounga leonina) and Weddell seals (Leptonychotes weddelli), that are top predatory marine mammals in the Antarctic ecosystem, using 16S rRNA amplicon sequencing and assessed the relationships of the gut microbial communities to functional profiles using gut metabolite analysis. The bacterial community did not differ significantly by host species or sex at the phylum level, but the distinction at the family level was obvious. The family Ruminococcaceae (Firmicutes) was more abundant in southern elephant seals than in Weddell seals, and the families Acidaminococcaceae (Firmicutes) and Pasteurellaceae (Gammaproteobacteria) were uniquely present in Weddell seals. The fecal bacterial community structure was distinctively clustered by host species, with only 6.7% of amplicon sequence variants (ASVs) shared between host species. This result implies that host phylogeny rather than other factors, such as diet or age, could be the major driver of fecal microbiotic diversification. Interestingly, there was no apparent sex effect on bacterial community structure in Weddell seals, but the effect of sex was pronounced in adult southern elephant seals mainly due to the prevalence of Edwardsiella sp., suggesting that extreme sexual dimorphism may modulate the gut microbiota of southern elephant seals. Unlike the clear distinction in the taxonomic composition of fecal bacterial communities, there were no discernible differences in the profiles of potential microbial functions and gut metabolites between host species or sexes, indicating that functional redundancy dominates the gut microbiota of seals surveyed in this study.

Characteristic and role of chromosomal type II toxin-antitoxin systems locus in Enterococcus faecalis ATCC29212: Zhen Li , Chao Shi , Shanjun Gao , Xiulei Zhang , Di Lu , Guangzhi Liu; J. Microbiol. 2020;58(12):1027-1036. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0079-3

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Abstract: The Gram-positive bacterium Enterococcus faecalis is currently one of the major pathogens of nosocomial infections. The lifestyle of E. faecalis relies primarily on its remarkable capacity to face and survive in harsh environmental conditions. Toxin-antitoxin (TA) systems have been linked to the growth control of bacteria in response to adverse environments but have rarely been reported in Enterococcus. Three functional type II TA systems were identified among the 10 putative TA systems encoded by E. faecalis ATCC29212. These toxin genes have conserved domains homologous to MazF (DR75_ 1948) and ImmA/IrrE family metallo-endopeptidases (DR75_ 1673 and DR75_2160). Overexpression of toxin genes could inhibit the growth of Escherichia coli. However, the toxin DR75_1673 could not inhibit bacterial growth, and the bacteriostatic effect occurred only when it was coexpressed with the antitoxin DR75_1672. DR75_1948–DR75_1949 and DR75_ 160–DR75_2161 could maintain the stable inheritance of the unstable plasmid pLMO12102 in E. coli. Moreover, the transcription levels of these TAs showed significant differences when cultivated under normal conditions and with different temperatures, antibiotics, anaerobic agents and H2O2. When DR75_2161 was knocked out, the growth of the mutant strain at high temperature and oxidative stress was limited. The experimental characterization of these TAs loci might be helpful to investigate the key roles of type II TA systems in the physiology and environmental stress responses of Enterococcus.

Characterization of the effects of terminators and introns on recombinant gene expression in the basidiomycete Ceriporiopsis subvermispora: Dong Xuan Nguyen , Emi Nishisaka , Moriyuki Kawauchi , Takehito Nakazawa , Masahiro Sakamoto , Yoichi Honda; J. Microbiol. 2020;58(12):1037-1045. Published online September 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0213-2

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Abstract: Terminators and introns are vital regulators of gene expression in many eukaryotes; however, the functional importance of these elements for controlling gene expression in Agaricomycetes remains unclear. In this study, the effects of Ceriporiopsis subvermispora terminators and introns on the expression of a recombinant hygromycin B phosphotransferase gene (hph) were characterized. Using a transient transformation system, we proved that a highly active terminator (e.g., the gpd terminator) is required for the efficient expression of the hph gene. Mutational analyses of the C. subvermispora gpd terminator revealed that hph expression was dictated by an A-rich region, which included a putative positioning element, and polyadenylation sites. In contrast, our results indicated that introns are not required for the expression of hph directed by the Csβ1-tub and Csgpd promoters in C. subvermispora. This study provides insights into the functions and cis-element requirements of transcriptional terminators in Agaricomycetes, which may be relevant for designing recombinant genes for this important fungal class.

Characterization of a novel dsRNA mycovirus of Trichoderma atroviride NFCF377 reveals a member of “Fusagraviridae” with changes in antifungal activity of the host fungus: Jeesun Chun , Byeonghak Na , Dae-Hyuk Kim; J. Microbiol. 2020;58(12):1046-1053. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0380-1

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Abstract: Trichoderma atroviride is a common fungus found in various ecosystems that shows mycoparasitic ability on other fungi. A novel dsRNA virus was isolated from T. atroviride NFCF377 strain and its molecular features were analyzed. The viral genome consists of a single segmented double-stranded RNA and is 9,584 bp in length, with two discontinuous open reading frames (ORF1 and ORF2). A mycoviral structural protein and an RNA-dependent RNA polymerase (RdRp) are encoded by ORF1 and ORF2, respectively, between which is found a canonical shifty heptameric signal motif (AAAAAAC) followed by an RNA pseudoknot. Analysis of sequence similarity and phylogeny showed that it is closely related to members of the proposed family “Fusagraviridae”, with a highest similarity to the Trichoderma atroviride mycovirus 1 (TaMV1). Although the sequence similarity of deduced amino acid to TaMV1 was evident, sequence deviations were distinctive at untranslated regions (UTRs) due to the extended size. Thus, we inferred this dsRNA to be a different strain of Trichoderma atroviride mycovirus 1 (TaMV1-NFCF377). Electron microscopy image exhibited an icosahedral viral particle of 40 nm diameter. Virus-cured isogenic isolates were generated and no differences in growth rate, colony morphology, or conidia production were observed between virus-infected and virus-cured strains. However, culture filtrates of TaMV1- NFCF377-infected strain showed enhanced antifungal activity against the plant pathogen Rhizoctonia solani but not to edible mushroom Pleurotus ostreatus. These results suggested that TaMV1-NFCF377 affected the metabolism of the fungal host to potentiate antifungal compounds against a plant pathogen, but this enhanced antifungal activity appeared to be species-specific.

Ganoderma boninense mycelia for phytochemicals and secondary metabolites with antibacterial activity: Syahriel Abdullah , Se-Eun Jang , Min-Kyu Kwak , KhimPhin Chong; J. Microbiol. 2020;58(12):1054-1064. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0208-z

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Abstract: Antiplasmodial nortriterpenes with 3,4-seco-27-norlanostane skeletons, almost entirely obtained from fruiting bodies, represent the main evidential source for bioactive secondary metabolites derived from a relatively unexplored phytopathogenic fungus, Ganoderma boninense. Currently lacking is convincing evidence for antimicrobial secondary metabolites in this pathogen, excluding that obtained from commonly observed phytochemicals in the plants. Herein, we aimed to demonstrate an efficient analytical approach for the production of antibacterial secondary metabolites using the mycelial extract of G. boninense. Three experimental cultures were prepared from fruiting bodies (GBFB), mycelium cultured on potato dextrose agar (PDA) media (GBMA), and liquid broth (GBMB). Through solvent extraction, culture type-dependent phytochemical distributions were diversely exhibited. Water-extracted GBMB produced the highest yield (31.21 ± 0.61%, p < 0.05), but both GBFB and GBMA elicited remarkably higher yields than GBMB when polar-organic solvent extraction was employed. Greater quantities of phytochemicals were also obtained from GBFB and GBMA, in sharp contrast to those gleaned from GBMB. However, the highest antibacterial activity was observed in chloroform-extracted GBMA against all tested bacteria. From liquid-liquid extractions (LLE), it was seen that mycelia extraction with combined chloroform-methanol-water at a ratio of 1:1:1 was superior at detecting antibacterial activities with the most significant quantities of antibacterial compounds. The data demonstrate a novel means of assessing antibacterial compounds with mycelia by LLE which avoids the shortcomings of standardized
method
ologies. Additionally, the antibacterial extract from the mycelia demonstrate that previously unknown bioactive secondary metabolites of the less studied subsets of Ganoderma may serve as active and potent antimicrobial compounds.

Biosynthesis of adipic acid in metabolically engineered Saccharomyces cerevisiae: Xi Zhang , Yingli Liu , Jing Wang , Yunying Zhao , Yu Deng; J. Microbiol. 2020;58(12):1065-1075. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0261-7

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Abstract: Adipic Acid (AA) is a valued platform chemical compound, which can be used as a precursor of nylon-6,6. Due to the generation of an enormous amount of nitric oxide metabolites and the growing depletion of oil resources as a result of AA production from a mixture of cyclohexanol and cyclohexanone, the microbial methods for synthesizing AA have attracted significant attention. Of the several AA-producing pathways, the reverse adipate degradation pathway in Thermobifida fusca (Tfu RADP) is reported to be the most efficient, which has been confirmed in Escherichia coli. In this study, the heterologous Tfu RADP was constructed for producing AA in S. cerevisiae by co-expressing genes of Tfu_ 0875, Tfu_2399, Tfu_0067, Tfu_1647, Tfu_2576, and Tfu_ 2576. The AA titer combined with biomass, cofactors and other by-products was all determined after fermentation. During batch fermentation in a shake flask, the maximum AA titer was 3.83 mg/L, while the titer increased to 10.09 mg/L during fed-batch fermentation in a 5-L bioreactor after fermentation modification.

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