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Schmitz M, Schultze A, Vanags R, Voigt K, Di Ventura B, Öztürk MA. patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures. Nucleic Acids Res 2022; 50:W560-W567. [PMID: 35438792 PMCID: PMC9252814 DOI: 10.1093/nar/gkac252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/11/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022] Open
Abstract
pH regulates protein function and interactions by altering the charge of individual residues causing loss or gain of intramolecular noncovalent bonds, which may lead to structural rearrangements. While tools to analyze residue-specific charge distribution of proteins at a given pH exist, currently no tool is available to investigate noncovalent bond changes at two different pH values. To make protein pH sensitivity analysis more accessible, we developed patcHwork, a web server that combines the identification of amino acids undergoing a charge shift with the determination of affected noncovalent bonds at two user-defined pH values. At the sequence-only level, patcHwork applies the Henderson–Hasselbalch equation to determine pH-sensitive residues. When the 3D protein structure is available, patcHwork can be employed to gain mechanistic understanding of the effect of pH. This is achieved using the PDB2PQR and PROPKA tools and noncovalent bond determination algorithms. A user-friendly interface allows visualizing pH-sensitive residues, affected salt bridges, hydrogen bonds and aromatic (pi–pi and cation–pi) interactions. patcHwork can be used to identify patches, a new concept we propose of pH-sensitive residues in close proximity on the protein, which may have a major impact on function. We demonstrate the attractiveness of patcHwork studying experimentally investigated pH-sensitive proteins (https://patchwork.biologie.uni-freiburg.de/).
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Affiliation(s)
- Mirko Schmitz
- Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.,Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Anne Schultze
- Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.,Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Raimonds Vanags
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.,Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Mehmet Ali Öztürk
- Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany.,Institute of Biology II, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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Okubo S, Terauchi K, Okada S, Saito Y, Yamaura T, Misaka T, Nakajima KI, Abe K, Asakura T. De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits. BMC Genomics 2021; 22:347. [PMID: 33985426 PMCID: PMC8120819 DOI: 10.1186/s12864-021-07674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Abstract
Background Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family members was unclear. Results Through de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and detailed analysis of the expression patterns of neoculin and neoculin-like genes in both species, we assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata, encoding both the basic and acidic subunits of neoculin in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in the two species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes differed considerably between the two species: the transcripts per million (TPM) values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in their expression profiles between C. latifolia and C. capitulata may be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07674-3.
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Affiliation(s)
- Satoshi Okubo
- The Yamashina Botanical Research Institute, Nippon Shinyaku Co., Ltd., Oyake Sakanotsuji-cho 39, Yamashina-ku, Kyoto, 607-8182, Japan
| | - Kaede Terauchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shinji Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoshikazu Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takao Yamaura
- The Yamashina Botanical Research Institute, Nippon Shinyaku Co., Ltd., Oyake Sakanotsuji-cho 39, Yamashina-ku, Kyoto, 607-8182, Japan
| | - Takumi Misaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ken-Ichiro Nakajima
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Present address: Division of Endocrinology and Metabolism, National Institute for Physiological Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Keiko Abe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan
| | - Tomiko Asakura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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