Journal of Microbiology

Review

[Minireview]Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches: Dae-Wi Kim , Jae-Hyung Ahn , Chang-Jun Cha; J. Microbiol. 2022;60(10):969-976. Published online September 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2313-7

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Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.

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Journal Articles

Structural and biochemical analysis of the PTPN4 PDZ domain bound to the C-terminal tail of the human papillomavirus E6 oncoprotein: Hye Seon Lee , Hye-Yeoung Yun , Eun-Woo Lee , Ho-Chul Shin , Seung Jun Kim , Bonsu Ku; J. Microbiol. 2022;60(4):395-401. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1606-1

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Abstract

High-risk genotypes of human papillomaviruses (HPVs) are directly implicated in various abnormalities associated with cellular hyperproliferation, including cervical cancer. E6 is one of two oncoproteins encoded in the HPV genome, which recruits diverse PSD-95/Dlg/ZO-1 (PDZ) domain-containing human proteins through its C-terminal PDZ-binding motif (PBM) to be degraded by means of the proteasome pathway. Among the three PDZ domain-containing protein tyrosine phosphatases, protein tyrosine phosphatase non-receptor type 3 (PTPN3) and PTPN13 were identified to be recognized by HPV E6 in a PBM-dependent manner. However, whether HPV E6 associates with PTPN4, which also has a PDZ domain and functions as an apoptosis regulator, remains undetermined. Herein, we present structural and biochemical evidence demonstrating the direct interaction between the PBM of HPV16 E6 and the PDZ domain of human PTPN4 for the first time. X-ray crystallographic structure determination and binding measurements using isothermal titration calorimetry demonstrated that hydrophobic interactions in which Leu158 of HPV16 E6 plays a key role and a network of intermolecular hydrogen bonds sustain the complex formation between PTPN4 PDZ and the PBM of HPV16 E6. In addition, it was verified that the corresponding motifs from several other highrisk HPV genotypes, including HPV18, HPV31, HPV33, and HPV45, bind to PTPN4 PDZ with comparable affinities, suggesting that PTPN4 is a common target of various pathogenic HPV genotypes.

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Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations
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Crystal Structures of Plk1 Polo-Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2-Derived Peptide
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Journal of Microbiology.2023; 61(8): 755. CrossRef
The effects of HPV oncoproteins on host communication networks: Therapeutic connotations
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Paraflavitalea soli gen. nov., sp. nov., isolated from greenhouse soil: Jun Heo , Hang-Yeon Weon , Hayoung Cho , Seung-Beom Hong , Jeong-Seon Kim , Soo-Jin Kim , Soon-Wo Kwon; J. Microbiol. 2020;58(1):17-23. Published online November 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9236-y

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Abstract

A bacterial strain designated 5GH32-13T was isolated from greenhouse soil in Yongin-city, Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, motile rods of two different shapes. The strain was catalase-positive and oxidasenegative. Flexirubin-like pigments were not detected. β-Carotene was produced. The strain grew in the range of 10–37°C (optimum of 28–30°C) and pH 6–8 (optimum of pH 7) and tolerated up to 1% (w/v) NaCl (optimum of 0%). According to the 16S rRNA gene sequence comparison, strain 5GH32- 13T shared a sequence similarity of less than 96.0% with all validly named taxa, having the highest sequence similarity with Pseudoflavitalea soli KIS20-3T (95.8%), Pseudoflavitalea rhizosphaerae T16R-265T (95.4%), Flavitalea gansuensis JCN-23T (95.3%), Pseudobacter ginsenosidimutans Gsoil 221T (95.3%), and Flavitalea populi HY-50RT (95.2%). A phylogenetic tree showed that strain 5GH32-13T was not grouped consistently into any specific genus. Its only polyamine was homospermidine, and its major fatty acids (> 10% of total fatty acids) were iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. The strain’s only respiratory quinone was MK-7, and its polar lipids were phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. Its DNA G + C content was 47.5 mol%. The results from chemotaxonomic, phenotypic and phylogenetic analyses indicated that strain 5GH32-13T represents a novel species of a novel genus of the family Chitinophagaceae, and the name Paraflavitalea soli gen. nov., sp. nov. is proposed. The type strain is 5GH32-13T (= KACC 17331T = JCM 33061T).

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

NOTE] Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. Belong to the Family Microbacteriaceae: Soo-Jin Kim , Jae-Hyung Ahn , Hang-Yeon Weon , Moriyuki Hamada , Ken-ichiro Suzuki , Soon-Wo Kwon; J. Microbiol. 2014;52(6):527-533. Published online February 17, 2014; DOI: https://doi.org/10.1007/s12275-014-3278-y

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Abstract

Two bacterial strains, KIS66-7T and 5GH26-15T, were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7T had the highest similarities with those of Labedella gwakjiensis KSW2-17T (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2SbT (97.2%), Leifsonia naganoensis JCM 10592T (97.0%), and Cryobacterium mesophilum MSL-15T (97.0%). Strain 5GH26-15T showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7T exhibited 96.4% similarity with that from 5GH26-15T. Strain KIS66-7T contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C15:0, ai-C17:0, and i-C16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C15:0, i-C16:0, and ai-C17:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7T and 5GH26-15T represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7T =KACC 15515T =NBRC 108724T) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15T =KACC 15524T =NBRC 108755T) within the family Microbacteriaceae.

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