Journal of Microbiology

Journal Article

Ship Hull‑Fouling Diatoms on Korean Research Vessels Revealed by Morphological and Molecular Methods, and Their Environmental Implications: Jaeyeong Park , Taehee Kim , Buhari Lawan Muhammad , Jang-Seu Ki; J. Microbiol. 2023;61(6):615-626. Published online May 25, 2023; DOI: https://doi.org/10.1007/s12275-023-00055-3

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Abstract: Ship biofouling is one of the main vectors for the introduction and global spread of non-indigenous organisms. Diatoms were the early colonizers of ship hulls; however, their community composition on ships is poorly understood. Herein, we investigated the diatom community on the hull samples collected from two Korean research vessels Isabu (IRV) and Onnuri (ORV) on September 2 and November 10, 2021, respectively. IRV showed low cell density (345 cells/cm2) compared to ORV (778 cells/cm2). We morphologically identified more than 15 species of diatoms from the two research vessels (RVs). The microalgae in both RVs were identified as Amphora, Cymbella, Caloneis, Halamphora, Navicula, Nitzschia, and Plagiogramma. Of them, the genus Halamphora was found to be predominant. However, both RVs had a varied dominant species with a significant difference in body size; Halamphora oceanica dominated at IRV, and Halamphora sp. at ORV, respectively. Molecular cloning showed similar results to morphological analysis, in which Halamphora species dominated in both RVs. The hull-attached species were distinct from species found in the water column. These results revealed diatoms communities that are associated with ship hull-fouling at an early stage of biofilm formation. Moreover, ships arriving from different regions could show some variation in species composition on their hull surfaces, with the potential for nonindigenous species introduction.

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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17 Citations

Abstract: 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.

Journal Article

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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6 Citations

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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