Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses
Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Kurt, Fırat [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2021 |
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| Schlagwörter: |
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| Anmerkung: |
© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 |
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| Übergeordnetes Werk: |
Enthalten in: Journal of plant growth regulation - New York, NY : Springer, 1982, 41(2021), 6 vom: 18. Juli, Seite 2246-2260 |
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| Übergeordnetes Werk: |
volume:41 ; year:2021 ; number:6 ; day:18 ; month:07 ; pages:2246-2260 |
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| DOI / URN: |
10.1007/s00344-021-10438-8 |
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SPR047641770 |
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| 100 | 1 | |a Kurt, Fırat |e verfasserin |4 aut | |
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| 520 | |a Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. | ||
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10.1007/s00344-021-10438-8 doi (DE-627)SPR047641770 (SPR)s00344-021-10438-8-e DE-627 ger DE-627 rakwb eng Kurt, Fırat verfasserin aut Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 Filiz, Ertugrul (orcid)0000-0001-9636-6389 aut Aydın, Adnan aut Enthalten in Journal of plant growth regulation New York, NY : Springer, 1982 41(2021), 6 vom: 18. Juli, Seite 2246-2260 (DE-627)254630448 (DE-600)1462091-1 1435-8107 nnns volume:41 year:2021 number:6 day:18 month:07 pages:2246-2260 https://dx.doi.org/10.1007/s00344-021-10438-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 41 2021 6 18 07 2246-2260 |
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10.1007/s00344-021-10438-8 doi (DE-627)SPR047641770 (SPR)s00344-021-10438-8-e DE-627 ger DE-627 rakwb eng Kurt, Fırat verfasserin aut Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 Filiz, Ertugrul (orcid)0000-0001-9636-6389 aut Aydın, Adnan aut Enthalten in Journal of plant growth regulation New York, NY : Springer, 1982 41(2021), 6 vom: 18. Juli, Seite 2246-2260 (DE-627)254630448 (DE-600)1462091-1 1435-8107 nnns volume:41 year:2021 number:6 day:18 month:07 pages:2246-2260 https://dx.doi.org/10.1007/s00344-021-10438-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 41 2021 6 18 07 2246-2260 |
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10.1007/s00344-021-10438-8 doi (DE-627)SPR047641770 (SPR)s00344-021-10438-8-e DE-627 ger DE-627 rakwb eng Kurt, Fırat verfasserin aut Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 Filiz, Ertugrul (orcid)0000-0001-9636-6389 aut Aydın, Adnan aut Enthalten in Journal of plant growth regulation New York, NY : Springer, 1982 41(2021), 6 vom: 18. Juli, Seite 2246-2260 (DE-627)254630448 (DE-600)1462091-1 1435-8107 nnns volume:41 year:2021 number:6 day:18 month:07 pages:2246-2260 https://dx.doi.org/10.1007/s00344-021-10438-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 41 2021 6 18 07 2246-2260 |
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10.1007/s00344-021-10438-8 doi (DE-627)SPR047641770 (SPR)s00344-021-10438-8-e DE-627 ger DE-627 rakwb eng Kurt, Fırat verfasserin aut Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 Filiz, Ertugrul (orcid)0000-0001-9636-6389 aut Aydın, Adnan aut Enthalten in Journal of plant growth regulation New York, NY : Springer, 1982 41(2021), 6 vom: 18. Juli, Seite 2246-2260 (DE-627)254630448 (DE-600)1462091-1 1435-8107 nnns volume:41 year:2021 number:6 day:18 month:07 pages:2246-2260 https://dx.doi.org/10.1007/s00344-021-10438-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 41 2021 6 18 07 2246-2260 |
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10.1007/s00344-021-10438-8 doi (DE-627)SPR047641770 (SPR)s00344-021-10438-8-e DE-627 ger DE-627 rakwb eng Kurt, Fırat verfasserin aut Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 Filiz, Ertugrul (orcid)0000-0001-9636-6389 aut Aydın, Adnan aut Enthalten in Journal of plant growth regulation New York, NY : Springer, 1982 41(2021), 6 vom: 18. Juli, Seite 2246-2260 (DE-627)254630448 (DE-600)1462091-1 1435-8107 nnns volume:41 year:2021 number:6 day:18 month:07 pages:2246-2260 https://dx.doi.org/10.1007/s00344-021-10438-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4328 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 AR 41 2021 6 18 07 2246-2260 |
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In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Sulphur</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Sulfite reductase</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Bioinformatics</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Molecular docking</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Filiz, Ertugrul</subfield><subfield code="0">(orcid)0000-0001-9636-6389</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Aydın, Adnan</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">Enthalten in</subfield><subfield code="t">Journal of plant growth regulation</subfield><subfield code="d">New York, NY : Springer, 1982</subfield><subfield code="g">41(2021), 6 vom: 18. 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Kurt, Fırat |
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Kurt, Fırat misc Sulphur misc Sulfite reductase misc Bioinformatics misc Molecular docking Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses |
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Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses Sulphur (dpeaa)DE-He213 Sulfite reductase (dpeaa)DE-He213 Bioinformatics (dpeaa)DE-He213 Molecular docking (dpeaa)DE-He213 |
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Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses |
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sulfite reductase (sir) gene in rice (oryza sativa): bioinformatics and expression analyses under salt and drought stresses |
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Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses |
| abstract |
Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 |
| abstractGer |
Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 |
| abstract_unstemmed |
Abstract Rice sulfite reductase (OsSiR) is important protein in reducing sulfite to sulfide. In this paper, it is aimed to shed light on OsSiR’s probable structure, function, and expression using in silico methods and test its responses under drought and salt stresses. Moreover, it was also analyzed if OsSiR was structurally different from other SiR proteins. We estimated that OsSiR lacks ribbon–helix–helix DNA-binding motif allowing it to bind to DNA; therefore, it was probably localized in stroma as a non-nucleoid-type protein. Also, we found that OsSiR expression was regulated by JA in roots and by crosstalk of JA and ABA in shoots. RT-qPCR results showed that there was 20% increase in the expression of OsSiR at 3rd h of the salt treatment. However, OsSiR was downregulated when exposed to drought stress and salt stress for longer periods of time, respectively. OsSiR has a high post-translational potential because of its high phosphorylation sites. This may be originating from the most prevalent residue, Gly, facilitating its binding to phosphates in OsSiR. Our docking results showed that ligand binding residues of OsSiR (Arg159, Thr162, Gln167, and Pro501) were also active site residues of OsSiR. Both two domains of OsSiR interacted with sulfite and the number of the residues in 4Fe–4S domain (PF01077) was higher. The findings in this study are important in terms of structural and expressional studies of rice SiR (OsSiR) and can be used for SiR proteins in sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica), which are closely related and highly similar to OsSiR in terms of sequence and predicted 3D structure. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021 |
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| title_short |
Sulfite Reductase (SiR) Gene in Rice (Oryza sativa): Bioinformatics and Expression Analyses Under Salt and Drought Stresses |
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https://dx.doi.org/10.1007/s00344-021-10438-8 |
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Filiz, Ertugrul Aydın, Adnan |
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10.1007/s00344-021-10438-8 |
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2024-07-03T14:03:02.773Z |
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| score |
7.3996353 |