Che Ok Jeon

Complete Genome Sequence of Leuconostoc mesenteroides subsp. mesenteroides Strain J18, Isolated from Kimchi

Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid bacterial groups during kimchi fermentation. Here, we report the complete genome sequence of L. mesenteroides subsp. mesenteroides J18, which was isolated from kimchi. The genome of the strain consists of a 1,896,561-bp chromosome and five plasmids.

Complete genome sequence of Weissella koreensis KACC 15510, isolated from kimchi.

Weissella koreensis KACC 15510 was isolated from kimchi, a representative traditional Korean fermented food. Here, we announce the complete genome sequence of W. koreensis KACC 15510, consisting of a 1,422,478-bp chromosome and one 18,992-bp plasmid, and provide a description of their annotation.

Complete Genome Sequence of Leuconostoc kimchii Strain C2, Isolated from Kimchi

Leuconostoc kimchii strain C2 was isolated from fermented kimchi in Korea. Here we announce the complete genome sequence of Leuconostoc kimchii strain C2, consisting of a 1,877,174-bp chromosome with a G+C content of 37.9% and no plasmid and describe major findings from its annotation.

Integrative view of 2-oxoglutarate/Fe(II)-dependent oxygenase diversity and functions in bacteria.

BACKGROUNDnThe 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites.nnnMETHODSnTo investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily.nnnRESULTSnThe network based on experimentally characterized 2OG oxygenases reflects functional clustering. Networks based on all of the bacterial 2OG oxygenases from the Interpro database indicate that only few proteins in this superfamily are functionally defined. The uneven distribution of the enzymes supports the hypothesis that horizontal gene transfer plays an important role in 2OG oxygenase evolution. A hydrophobic tyrosine residue binding the primary substrates at the N-termini is conserved. At the C-termini, the iron-binding, oxoglutarate-binding, and hydrophobic motifs are conserved and coevolved. Considering the proteins in the family are largely unexplored, we annotated them by the Pfam database and hundreds of novel and multi-domain proteins are discovered. Among them, a two-domain protein containing an N-terminal peroxiredoxin domain and a C-terminal 2OG oxygenase domain was characterized enzymatically. The results show that the enzyme could catalyze the reduction of peroxide using 2-oxoglutarate as an electron donor.nnnCONCLUSIONSnOur observations suggest relatively low evolutionary pressure on the bacterial 2OG oxygenases and a straightforward electron transfer pathway catalyzed by the two-domain 2OG oxygenase.nnnGENERAL SIGNIFICANCEnThis work enables an expanded understanding of the diversity, evolution, and functions of bacterial 2OG oxygenases.

A Zinc-Dependent Protease AMZ-tk from a Thermophilic Archaeon is a New Member of the Archaemetzincin Protein Family

A putative zinc-dependent protease (TK0512) in Thermococcus kodakarensis KOD1 shares a conserved motif with archaemetzincins, which are metalloproteases found in archaea, bacteria, and eukarya. Phylogenetic and sequence analyses showed that TK0512 and its homologues in Thermococcaceae represent new members in the archaemetzincins family, which we named AMZ-tk. We further confirmed its proteolytic activity biochemically by overexpression of the recombinant AMZ-tk in Escherichia coli and characterization of the purified enzyme. In the presence of zinc, the purified enzyme degraded casein, while adding EDTA strongly inhibited the enzyme activity. AMZ-tk also exhibited self-cleavage activity that required Zn2+. These results demonstrated that AMZ-tk is a zinc-dependent protease within the archaemetzincin family. The enzyme displayed activity at alkaline pHs ranging from 7.0 to 10.0, with the optimal pH being 8.0. The optimum temperature for the catalytic activity of AMZ-tk was 55°C. Quantitative reverse transcription-PCR revealed that transcription of AMZ-tk was also up-regulated after exposing the cells to 55 and 65°C. Mutant analysis suggested that Zn2+ binding histidine and catalytic glutamate play key roles in proteolysis. AMZ-tk was thermostable on incubation for 4 h at 70°C in the presence of EDTA. AMZ-tk also retained >50% of its original activity in the presence of both laboratory surfactants and commercial laundry detergents. AMZ-tk further showed antibacterial activity against several bacteria. Therefore, AMZ-tk is of considerable interest for many purposes in view of its activity at alkaline pH, detergents, and thermostability.

Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa

BACKGROUNDnThe 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily in Metazoa is responsible for protein modification, nucleic acid repair and/or modification, and fatty acid metabolism.nnnMETHODSnPhylogenetic analysis, protein sequence similarity network (SSN) and other bioinformatics tools were used to analyze the evolutionary relationship and make functional inferences of Metazoa 2OG oxygenases.nnnRESULTSnSixty-four 2OG oxygenases have been previously found in Homo sapiens; they catalyze two reactions: hydroxylation and demethylation. Phylogenetic analyses indicated that enzymes with similar domain architecture are always clustered together, and the redox function can be performed by the 2OG oxygenase domain or Jumonji C (JmjC) domain, where the JmjC domain is always fused to other functional domains. We used the SSN to make functional inferences and to conduct distribution analysis of Metazoa 2OG oxygenases. >11,000 putative 2OG oxygenases across Metazoa could be assigned potential functions based on the SSN. The multiple sequence alignments showed that the residues binding iron are most highly conserved in both the 2OG oxygenase domain and JmjC domain. In contrast, the residues binding oxoglutarate are quite different in the two domains: the 2OG oxygenase domain tends to have an Arg/Lys at the C terminus, whereas the JmjC domain, an Asn/Lys residue in the middle region.nnnCONCLUSIONSnThe results indicated that gene duplication and vertical gene transfer have played important roles in 2OG oxygenase evolution in Metazoa and clarified the difference between the 2OG oxygenase domain and JmjC domain.nnnGENERAL SIGNIFICANCEnThese findings expand the understanding of the diversity, evolution, and functions of 2OG oxygenases.

Integrative view of the diversity and evolution of SWEET and semiSWEET sugar transporters

Sugars Will Eventually be Exported Transporter (SWEET) and SemiSWEET are recently characterized families of sugar transporters in eukaryotes and prokaryotes, respectively. SemiSWEETs contain 3 transmembrane helices (TMHs), while SWEETs contain 7. Here, we performed sequence-based comprehensive analyses for SWEETs and SemiSWEETs across the biosphere. In total, 3,249 proteins were identified and ≈60% proteins were found in green plants and Oomycota, which include a number of important plant pathogens. Protein sequence similarity networks indicate that proteins from different organisms are significantly clustered. Of note, SemiSWEETs with 3 or 4 TMHs that may fuse to SWEET were identified in plant genomes. 7-TMH SWEETs were found in bacteria, implying that SemiSWEET can be fused directly in prokaryote. 15-TMH extraSWEET and 25-TMH superSWEET were also observed in wild rice and oomycetes, respectively. The transporters can be classified into 4, 2, 2, and 2 clades in plants, Metazoa, unicellular eukaryotes, and prokaryotes, respectively. The consensus and coevolution of amino acids in SWEETs were identified by multiple sequence alignments. The functions of the highly conserved residues were analyzed by molecular dynamics analysis. The 19 most highly conserved residues in the SWEETs were further confirmed by point mutagenesis using SWEET1 from Arabidopsis thaliana. The results proved that the conserved residues located in the extrafacial gate (Y57, G58, G131, and P191), the substrate binding pocket (N73, N192, and W176), and the intrafacial gate (P43, Y83, F87, P145, M161, P162, and Q202) play important roles for substrate recognition and transport processes. Taken together, our analyses provide a foundation for understanding the diversity, classification, and evolution of SWEETs and SemiSWEETs using large-scale sequence analysis and further show that gene duplication and gene fusion are important factors driving the evolution of SWEETs.

New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes

Sugars will eventually be exported transporters (SWEETs) and SemiSWEETs represent a family of sugar transporters in eukaryotes and prokaryotes, respectively. SWEETs contain seven transmembrane helices (TMHs), while SemiSWEETs contain three. The functions of SemiSWEETs are less studied. In this perspective article, we analyzed the diversity and conservation of SemiSWEETs and further proposed the possible functions. 1,922 SemiSWEET homologs were retrieved from the UniProt database, which is not proportional to the sequenced prokaryotic genomes. However, these proteins are very diverse in sequences and can be classified into 19 clusters when >50% sequence identity is required. Moreover, a gene context analysis indicated that several SemiSWEETs are located in the operons that are related to diverse carbohydrate metabolism. Several proteins with seven TMHs can be found in bacteria, and sequence alignment suggested that these proteins in bacteria may be formed by the duplication and fusion. Multiple sequence alignments showed that the amino acids for sugar translocation are still conserved and coevolved, although the sequences show diversity. Among them, the functions of a few amino acids are still not clear. These findings highlight the challenges that exist in SemiSWEETs and provide future researchers the foundation to explore these uncharted areas.