Journal of Microbiology

Volume 57(4); April 2019

Review

[MINIREVIEW] The nature of meiotic chromosome dynamics and recombination in budding yeast: Soogil Hong , Jeong Hwan Joo , Hyeseon Yun , Keunpil Kim; J. Microbiol. 2019;57(4):221-231. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8541-9

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Abstract: During meiosis, crossing over allows for the exchange of genes between homologous chromosomes, enabling their segregation and leading to genetic variation in the resulting gametes. Spo11, a topoisomerase-like protein expressed in eukaryotes, and diverse accessory factors induce programmed doublestrand breaks (DSBs) to initiate meiotic recombination during the early phase of meiosis after DNA replication. DSBs are further repaired via meiosis-specific homologous recombination. Studies on budding yeast have provided insights into meiosis and genetic recombination and have improved our understanding of higher eukaryotic systems. Cohesin, a chromosome-associated multiprotein complex, mediates sister chromatid cohesion (SCC), and is conserved from yeast to humans. Diverse cohesin subunits in budding yeast have been identified in DNA metabolic pathways, such as DNA replication, chromosome segregation, recombination, DNA repair, and gene regulation. During cell cycle, SCC is established by multiple cohesin subunits, which physically bind sister chromatids together and modulate proteins that involve in the capturing and separation of sister chromatids. Cohesin components include at least four core subunits that establish and maintain SCC: two structural maintenance chromosome subunits (Smc1 and Smc3), an α-kleisin subunit (Mcd1/Scc1 during mitosis and Rec8 during meiosis), and Scc3/Irr1 (SA1 and SA2). In addition, the cohesin-associated factors Pds5 and Rad61 regulate structural modifications and cell cyclespecific dynamics of chromatin to ensure accurate chromosome segregation. In this review, we discuss SCC and the recombination pathway, as well as the relationship between the two processes in budding yeast, and we suggest a possible conserved mechanism for meiotic chromosome dynamics from yeast to humans.

Journal Articles

Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond: Tingye Feng , Sang Eun Jeong , Jin Ju Lim , Seogang Hyun , Che Ok Jeon; J. Microbiol. 2019;57(4):232-237. Published online January 16, 2019; DOI: https://doi.org/10.1007/s12275-019-8463-6

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Abstract: A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27T was observed at 20–40°C (optimum, 30°C), pH 5.0–7.0 (optimum, pH 6.0), and 0–0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C16:0, cyclo-C17:0, and cyclo- C19:0 ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27T was most closely related to Paraburkholderia rhynchosiae WSM3937T, Paraburkholderia ginsengiterrae DCY85T, Paraburkholderia fungorum NBRC 102489T, and Paraburkholderia graminis C4D1MT with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27T (KACC 19714 T = JCM 32721T).

Mesorhizobium denitrificans sp. nov., a novel denitrifying bacterium isolated from sludge: Muhammad Zubair Siddiqi , Ngo Thi Phuong Thao , Gyumin Choi , Dae-Cheol Kim , Young-Woo Lee , Sang Young Kim , Ji-Hyang Wee , Wan-Taek Im; J. Microbiol. 2019;57(4):238-242. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8590-0

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Abstract: A Gram-stain-negative, non-spore-forming, facultative, rodshaped bacterium (designated LA-28T) was isolated from a sludge sample from a wastewater treatment plant in Hanam city, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain LA-28T clustered with species of the genus Mesorhizobium and appeared closely related to M. jarvisii LMG 28313T (96.8%), M. waimense ICMP 19557T (96.7%), and M. huakuii LMG 14107T (96.7%). Growth occurs at 18– 40°C on R2A medium in the presence of 1–4% NaCl (w/v) and at pH 6–8. The DNA G+C content was 61.2 mol%, and the predominant quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (> 5%) were C16:0, C19:0 ω8c cyclo, C18:1 ω7c 11-methyl, and C18:1 ω7c and/or C18:1 ω6c (summed feature 8). Major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidyl-N-methylethanolamine (PME), and phosphatidylcholine (PC). Physiological and biochemical characteristics indicated that strain LA-28T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium denitrificans sp. nov. is proposed. The type strain is LA-28T (= KACC 19675T = LMG 30806T).

Growth of cyanobacterial soil crusts during diurnal freeze-thaw cycles: Steven K. Schmidt , Lara Vimercati; J. Microbiol. 2019;57(4):243-251. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8359-5

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Abstract: Various Nostoc spp. and related cyanobacteria are able to survive extreme temperatures and are among the most successful colonists of high-elevation sites being exposed due to glacial retreat. It is unclear, however, if cyanobacteria can grow during the extreme freeze-thaw cycles that occur on a yearround basis at high-elevation, peri-glacial sites or if they only grow during the rare periods when freeze-thaw cycles do not occur. We conducted several experiments to determine if cyanobacteria that form biological soil crusts (BSCs) at highelevation sites (> 5,000 m.a.s.l.) in the Andes can grow during diurnal freeze-thaw cycles on a par with those that occur in the field. Here we show that a soil crust that had been frozen at -20°C for five years was able to increase from 40% to 100% soil coverage during a 45-day incubation during which the soil temperature cycled between -12°C and 26°C every day. In a second, experiment an undeveloped soil with no visible BSCs showed a statistically significant shift in the bacterial community from one containing few cyanobacterial sequences (8% of sequences) to one dominated (27%) by Nostoc, Microcoleus, and Leptolyngbya phylotypes during a 77-day incubation with daily freeze-thaw cycles. In addition, counts of spherical Nostoc-like colonies increased significantly on the soil surface during the experiment, especially in microcosms receiving phosphorus. Taken together these results show that freeze-thaw cycles alone do not limit the growth of BSCs in high-elevation soils, and provide new insight into how life is able to thrive in one of the most extreme terrestrial environments on Earth.

Co-occurrence patterns between phytoplankton and bacterioplankton across the pelagic zone of Lake Baikal during spring: Ivan S. Mikhailov , Yuri S. Bukin , Yulia R. Zakharova , Marina V. Usoltseva , Yuri P. Galachyants , Maria V. Sakirko , Vadim V. Blinov , Yelena V. Likhoshway; J. Microbiol. 2019;57(4):252-262. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8531-y

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Abstract: Phytoplankton and bacterioplankton play a key role in carbon cycling of aquatic ecosystems. In this study, we found that co-occurrence patterns between different types of phytoplankton, bacterioplankton, and environmental parameters in Lake Baikal during spring were different over the course of three consecutive years. The composition of phytoplankton and bacterial communities was investigated using microscopy and 16S rRNA gene pyrosequencing, respectively. Non-metric multidimensional scaling (NMDS) revealed a relationship between the structure of phytoplankton and bacterial communities and temperature, location, and sampling year. Associations of bacteria with diatoms, green microalgae, chrysophyte, and cryptophyte were identified using microscopy. Cluster analysis revealed similar correlation patterns between phytoplankton abundance, number of attached bacteria, ratio of bacteria per phytoplankton cell and environmental parameters. Positive and negative correlations between different species of phytoplankton, heterotrophic bacteria and environmental parameters may indicate mutualistic or competitive relationships between microorganisms and their preferences to the environment.

β-1,3-Glucan/CR3/SYK pathway-dependent LC3B-II accumulation enhanced the fungicidal activity in human neutrophils: Ding Li , Changsen Bai , Qing Zhang , Zheng Li , Di Shao , Xichuan Li; J. Microbiol. 2019;57(4):263-270. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8298-1

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Abstract: Since molecular genotyping has been established for the Candida species, studies have found that a single Candida strain (endemic strain) can persist over a long period of time and results in the spread of nosocomial invasive candidiasis without general characteristics of horizontal transmissions. Our previous study also found the existence of endemic strains in a cancer center in Tianjin, China. In the current study, we performed further investigation on endemic and non-endemic Candida albicans strains, with the aim of explaining the higher morbidity of endemic strains. In an in vivo experiment, mice infected with endemic strains showed significantly shorter survival time and higher kidney fungal burdens compared to mice infected with non-endemic strains. In an in vitro experiment, the killing percentage of neutrophils to endemic strains was significantly lower than that to non-endemic strains, which is positively linked to the ratio of LC3B-II/I in neutrophils. An immunofluorescence assay showed more β-1,3-glucan exposure on the cell walls of nonendemic strains compared to endemic strains. After blocking the β-glucan receptor (CR3) or inhibiting downstream kinase (SYK) in neutrophils, the killing percent to C. albicans (regardless of endemic and non-endemic strains) and the ratio of LC3B-II/I of neutrophils were significantly decreased. These data suggested that the killing capability of neutrophils to C. albicans was monitored by β-1,3-glucan via CR3/SYK pathway-dependent LC3B-II accumulation and provided an explanation for the variable killing capability of neutrophils to different strains of C. albicans, which would be beneficial in improving infection control and therapeutic strategies for invasive candidiasis.

Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico: Enrique Jesús Delgado-Suárez , Rocío Ortíz-López , Wondwossen A. Gebreyes , Marc W. Allard , Francisco Barona-Gómez , María Salud Rubio-Lozano; J. Microbiol. 2019;57(4):271-280. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8421-3

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Abstract: Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is increasingly common worldwide. While food animals are thought to contribute to the growing antimicrobial resistance (AMR) problem, limited data is documenting this relationship, especially in low and middle-income countries (LMIC). Herein, we aimed to assess the role of non-clinical NTS of bovine origin as reservoirs of AMR genes of human clinical significance. We evaluated the phenotypic and genotypic AMR profiles in a set of 44 bovine-associated NTS. For comparative purposes, we also included genotypic AMR data of additional isolates from Mexico (n = 1,067) that are publicly available. The most frequent AMR phenotypes in our isolates involved tetracycline (40/44), trimethoprim-sulfamethoxazole (26/44), chloramphenicol (19/44), ampicillin (18/44), streptomycin (16/44), and carbenicillin (13/44), while nearly 70% of the strains were MDR. These phenotypes were correlated with a widespread distribution of AMR genes (i.e. tetA, aadA, dfrA12, dfrA17, sul1, sul2, bla-TEM-1, blaCARB-2) against multiple antibiotic classes, with some of them contributed by plasmids and/or class-1 integrons. We observed different AMR genotypes for betalactams and tetracycline resistance, providing evidence of convergent evolution and adaptive AMR. The probability of MDR genotype occurrence was higher in meat-associated isolates than in those from other sources (odds ratio 11.2, 95% confidence interval 4.5–27.9, P < 0.0001). The study shows that beef cattle are a significant source of MDR NTS in Mexico, highlighting the role of animal production on the emergence and spread of MDR Salmonella in LMIC.

Analysis of the L-malate biosynthesis pathway involved in poly(β-L-malic acid) production in Aureobasidium melanogenum GXZ-6 by addition of metabolic intermediates and inhibitors: Wei Zeng , Bin Zhang , Qi Liu , Guiguang Chen , Zhiqun Liang; J. Microbiol. 2019;57(4):281-287. Published online February 5, 2019; DOI: https://doi.org/10.1007/s12275-019-8424-0

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Abstract: Poly(β-L-malic acid) (PMA) is a promising polyester formed from L-malate in microbial cells. Malate biosynthesis is crucial for PMA production. Previous studies have shown that the non-oxidative pathway or oxidative pathway (TCA cycle) is the main biosynthetic pathway of malate in most of PMAproducing strains, while the glyoxylate cycle is only a supplementary pathway. In this study, we investigated the effect of exogenous metabolic intermediates and inhibitors of the malate biosynthetic pathway on PMA production by Aureobasidium melanogenum GXZ-6. The results showed that PMA production was stimulated by maleic acid (a fumarase inhibitor) and sodium malonate (a succinate dehydrogenase inhibitor) but inhibited by succinic acid and fumaric acid. This indicated that the TCA cycle might not be the only biosynthetic pathway of malate. In addition, the PMA titer increased by 18.1% upon the addition of glyoxylic acid after 72 h of fermentation, but the PMA titer decreased by 7.5% when itaconic acid (an isocitrate lyase inhibitor) was added, which indicated that malate for PMA production was synthesized significantly via the glyoxylate cycle rather than the TCA cycle. Furthermore, in vitro enzyme activities of the TCA and glyoxylate cycles suggested that the glyoxylate cycle significantly contributed to the PMA production, which is contradictory to what has been reported previously in other PMA-producing A. pullulans.

Antimicrobial effect and proposed action mechanism of cordycepin against Escherichia coli and Bacillus subtilis: Qi Jiang , Zaixiang Lou , Hongxin Wang , Chen Chen; J. Microbiol. 2019;57(4):288-297. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8113-z

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Abstract: The detailed antibacterial mechanism of cordycepin efficacy against food-borne germs remains ambiguous. In this study, the antibacterial activity and action mechanism of cordycepin were assessed. The results showed that cordycepin effectively inhibited the growth of seven bacterial pathogens including both Gram-positive and Gram-negative bacterial pathogens; the minimum inhibitory concentrations (MIC) were 2.5 and 1.25 mg/ml against Escherichia coli and Bacillus subtilis, respectively. Scanning electron microscope and transmission electron microscope examination confirmed that cordycepin caused obvious damages in the cytoplasmatic membranes of both E. coli and B. subtilis. Outer membrane permeability assessment indicated the loss of barrier function and the leakage of cytoplasmic contents. Propidium iodide and carboxyfluorescein diacetate double staining approach coupled with flow cytometry analysis indicated that the integrity of cell membrane was severely damaged during a short time, while the intracellular enzyme system still remained active. This clearly suggested that membrane damage was one of the reasons for cordycepin efficacy against bacteria. Additionally, results from circular dichroism and fluorescence analysis indicated cordycepin could insert to genome DNA base and double strand, which disordered the structure of genomic DNA. Basis on these results, the mode of bactericidal action of cordycepin against E. coli and B. subtilis was found to be a dual mechanism, disrupting bacterial cell membranes and binding to bacterial genomic DNA to interfere in cellular functions, ultimately leading to cell death.

Role of putative virulence traits of Campylobacter jejuni in regulating differential host immune responses: Ankita Singh , Amirul Islam Mallick; J. Microbiol. 2019;57(4):298-309. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8165-0

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Abstract: Among the major enteric pathogens, Campylobacter jejuni is considered an important source of diarrheal illness in humans. In contrast to the acute gastroenteritis in humans, C. jejuni exhibits prolonged cecal colonization at a high level with little or no pathology in chickens. Although several known virulence determinants of C. jejuni have been found to be associated with a higher degree of pathogenesis in humans, to date, little is known about their functions in the persistent colonization of chickens. The present study was undertaken to assess the role of C. jejuni in imparting differential host immune responses in human and chicken cells. Based on the abundance of major genes encoding virulence factors (GEVFs), we used a particular isolate that harbors the cadF, flaA, peb1, racR, ciaB, cdtB, and hcp genes. This study showed that hypervirulent C. jejuni isolate that encodes a functional type VI secretion system (T6SS) has a greater ability to invade and create characteristic “attaching and effacing” lesions in human INT407 compared to primary chicken embryo intestinal cells (CEICs). Furthermore, we demonstrated that the higher bacterial invasion in human INT407 triggered higher levels of expression of major proinflammatory cytokines, such as IL- 1β and IL-6, and significant downregulation of IL-17A gene expression (P ≤ 0.05). The findings of the present study suggest that the enhanced ability of C. jejuni to invade human cells is tightly regulated by proinflammatory cytokines in the gut and possibly holds the keys to the observed differences in pathogenesis between human and chicken cells.

Lipoteichoic acids of lactobacilli inhibit Enterococcus faecalis biofilm formation and disrupt the preformed biofilm: Solmin Jung , Ok-Jin Park , A Reum Kim , Ki Bum Ahn , Dongwook Lee , Kee-Yeon Kum , Cheol-Heui Yun , Seung Hyun Han; J. Microbiol. 2019;57(4):310-315. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8538-4

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41 Citations

Abstract: Enterococcus faecalis, a Gram-positive bacterium commonly isolated in patients with refractory apical periodontitis, invades dentin tubules easily and forms biofilms. Bacteria in biofilms, which contribute to recurrent and/or chronic inflammatory diseases, are more resistant to antimicrobial agents than planktonic cells and easily avoid phagocytosis. Although Lactobacillus plantarum lipoteichoic acid (Lp.LTA) is associated with biofilm formation, the effect of Lp.LTA on biofilm formation by E. faecalis is not clearly understood. In this study, we investigated whether Lp.LTA inhibits E. faecalis biofilm formation. The degree of biofilm formation was determined by using crystal violet assay and LIVE/DEAD bacteria staining. The quantification of bacterial growth was determined by measuring the optical density at 600 nm with a spectrophotometer. Formation of biofilms on human dentin slices was observed under a scanning electron microscope. E. faecalis biofilm formation was reduced by Lp.LTA treatment in a dose-dependent manner. Lp.LTA inhibited biofilm development of E. faecalis at the early stage without affecting bacterial growth. LTA from other Lactobacillus species such as Lactobacillus acidophilus, Lactobacillus casei, or Lactobacillus rhamnosus GG also inhibited E. faecalis biofilm formation. In particular, among LTAs from various lactobacilli, Lp.LTA showed the highest inhibitory effect on biofilms formed by E. faecalis. Interestingly, LTAs from lactobacilli could remove the biofilm preformed by E. faecalis. These inhibitory effects were also observed on the surface of human dentin slices. In conclusion, Lactobacillus species LTA inhibits biofilm formation caused by E. faecalis and it could be used as an anti-biofilm agent for prevention or treatment against E. faecalis-associated diseases.

Genetic characterization of African swine fever virus in Cameroon, 2010–2018: Abel Wade , Jenna Elizabeth Achenbach , Carmina Gallardo , Tirumala Bharani K. Settypalli , Abdoulkadiri Souley , Gaston Djonwe , Angelika Loitsch , Gwenaelle Dauphin , Jean Justin Essia Ngang , Onana Boyomo , Giovanni Cattoli , Adama Diallo , Charles Euloge Lamien; J. Microbiol. 2019;57(4):316-324. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8457-4

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Abstract: African swine fever (ASF) is a highly lethal haemorrhagic disease in domestic and wild swine that has acquired great importance in sub-Saharan Africa since 1997. ASF was first reported in Cameroon in 1982 and was detected only in Southern Cameroon (South, West, East, Northwest, Southwest, Littoral, and Centre regions) until February 2010 when suspected ASF outbreaks were reported in the North and Far North regions. We investigated those outbreaks by analysing samples that were collected from sick pigs between 2010 and 2018. We confirmed 428 positive samples by ELISA and realtime PCR and molecularly characterized 48 representative isolates. All the identified virus isolates were classified as ASFV genotype I based on the partial B646L gene (C-terminal end of VP72 gene) and the full E183L gene encoding p54 protein analysis. Furthermore, analysis of the central variable region (CVR) within the B602L gene demonstrated that there were 3 different variants of ASFV genotype I, with 19, 20, and 21 tetrameric tandem repeat sequences (TRSs), that were involved in the 2010–2018 outbreaks in Cameroon. Among them, only variant A (19 TRSs) was identical to the Cam/82 isolate found in the country during the first outbreaks in 1981–1982. This study demonstrated that the three variants of ASFV isolates involved in these outbreaks were similar to those of neighbouring countries, suggesting a movement of ASFV strains across borders. Designing common control measures in affected regions and providing a compensation programme for farmers will help reduce the incidence and spread of this disease.

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