Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway

Jia, Baolei; Jia, Xiaomeng; Kim, Kyung Hyun; Pu, Zhong Ji; Kang, Myung-Suk; Jeon, Che Ok

doi:10.1038/srep43489

Cited by 20 publications

(13 citation statements)

References 64 publications

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“…On the other hand, the presence of glucose in the binding pocket increases the flexibility of the entire OsSWEET2b molecule, mainly due to changes in the TMH1 region and in the region from TMH5 to TMH6. Unlike soluble enzymes that have reduced flexibility after binding substrates (Jia et al, 2017a ), the binding of substrates to transporters always increases the flexibility of the proteins. This is seen in the biotin transporter of Rhodobacter capsulatus (Finkenwirth et al, 2015 ), an amino acid antiporter of Bacillus subtilis (Bippes et al, 2009 ) and lactose permease of E. coli (Serdiuk et al, 2014 ).…”

Section: Discussionmentioning

confidence: 99%

“…SSNs based on the retrieved proteins were constructed using the Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) (Gerlt et al, 2015 ) and visualized using Cytoscape 3.3 (Shannon et al, 2003 ). Each node in the network represents a protein, and an edge indicates that the two nodes connected by that edge are significantly similar, having an e -value less than the selected cutoff (Jia et al, 2017a , b , c ).…”

Section: Methodsmentioning

confidence: 99%

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Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters

Jia

Zhu

et al. 2017

Front. Plant Sci.

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters

Jia

Zhu

et al. 2017

Front. Plant Sci.

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“…The input metazoan sequences were retrieved from the InterPro database. In an SSN, each node indicates a protein, whereas the edge indicates that the 2 nodes share significant similarity with an e-value less than the selected cutoff (23)(24)(25).…”

Section: Construction Of the Ssnsmentioning

confidence: 99%

New insight into the classification and evolution of glucose transporters in the Metazoa

et al. 2019

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Because glucose is an essential energy source for living organisms, glucose transporters (GLUTs) are present in all species worldwide. Encoded by the solute carrier family 2 gene family, the GLUT proteins generally have 12 transmembrane helices (TMHs). In total, 14 GLUT proteins have been identified in humans (hGLUTs), and they are divided into 3 classes on the basis of their transport characteristics and sequence similarities. Herein, we report the use of protein sequence similarity networks (SSNs) to visualize the sequence trends of 4101 GLUT proteins across the Metazoa. The SSNs separated the metazoan proteins into 3 new classes that were different from the traditional classification system. In the new system, 9 of the 14 hGLUTs (hGLUT1–5, 7, 9, 11, and 14) were grouped into class I, 3 (hGLUT10, 12, and 13) were grouped into class II, and 2 (hGLUT6 and 8) were grouped into class III, as also supported by the phylogenetic tree. Multiple sequence alignments further showed that the conserved residues in each class were different. Furthermore, the hGLUTs in each class showed unique evolutionary characteristics, with similar nonsynonymous‐to‐synonymous divergence ratios and similar regions under conservative selection pressure. Of note, GLUTs with 3, 6, 18, 24, and 36 TMHs were identified among the metazoan genomes, and 1 Chinese hamster protein with 6 TMHs showed GLUT activity. In summary, this large‐scale sequence analysis provided new insights into the classification and evolution of GLUTs and further showed that gene duplication and fusion could have been important drivers during the evolution of these transporter molecules.—Jia, B., Yuan, D. P., Lan, W. J., Xuan, Y. H., Jeon, C. O. New insight into the classification and evolution of glucose transporters in the Metazoa. FASEB J. 33, 7519–7528 (2019). http://www.fasebj.org

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“…In addition to the naphthalene/PAH dioxygenases, two types of salicylate oxygenases responsible for conversion of salicylate and methylsalicylates to catechol were also detected in the active degrader, indicating that the uncultured Gammaproteobacterium sp. (bin5) could use salicylate oxygenase to catalyse the conversion of salicylate to catechol in the NAP degradation pathway (Cho et al ., 2005; Jia et al ., 2017).…”

Section: Discussionmentioning

confidence: 99%

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Cai

Guan

et al. 2021

Environmental Microbiology

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Summary Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable‐isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the 13C‐DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non‐culturable microorganisms by combining both SIP and metagenome binning.

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Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway

Cited by 20 publications

References 64 publications

Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters

Integrative View of the Diversity and Evolution of SWEET and SemiSWEET Sugar Transporters

New insight into the classification and evolution of glucose transporters in the Metazoa

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

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