Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B
This investigation involved a comparative analysis of the small GTPase superfamily in <i>S. lycopersicum</i> super strain B compared to their analogues in leguminous and other non-leguminous species. The small GTPases superfamily members were recognized by tBLASTn searches. The sequences...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-02-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/5/641 |
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| author | Hassan S. Al-Zahrani Tarek A. A. Moussa Hameed Alsamadany Rehab M. Hafez Michael P. Fuller |
| author_facet | Hassan S. Al-Zahrani Tarek A. A. Moussa Hameed Alsamadany Rehab M. Hafez Michael P. Fuller |
| author_sort | Hassan S. Al-Zahrani |
| collection | DOAJ |
| description | This investigation involved a comparative analysis of the small GTPase superfamily in <i>S. lycopersicum</i> super strain B compared to their analogues in leguminous and other non-leguminous species. The small GTPases superfamily members were recognized by tBLASTn searches. The sequences of amino acid were aligned using Clustal Omega and the analysis of phylogeny was performed with the MEGA7 package. Protein alignments were applied for all studied species. Three-dimensional models of RABA2, ROP9, and ROP10 from <i>Solanum lycopersicum</i> “Super strain B” were performed. The levels of mRNA of the Rab, Arf, Rop, and Ran subfamilies were detected in aerial tissues vs. roots. Significant divergences were found in the number of members and groups comprising each subfamily of the small GTPases and <i>Glycine max</i> had the highest count. High expression of Rab and Arf proteins was shown in the roots of legumes whilst in non-legume plants, the highest values were recorded in aerial tissues. <i>S. lycopersicum</i> super strain B had the highest expression of Rab and Arf proteins in its aerial tissues, which may indicate that diazotroph strains have supreme activities in the aerial tissues of strain B and act as associated N-fixing bacteria. The phylogenies of the small GTPase superfamily of the studied plants did not reveal asymmetric evolution of the Ra, Arf, Rop, and Ran subfamilies. Multiple sequence alignments derived from each of the Rab, Arf, and Rop proteins of <i>S. lycopersicum</i> super strain B showed a low frequency of substitutions in their domains. GTPases superfamily members have definite functions during infection, delivery, and maintenance of N<sub>2</sub>-fixing diazotroph but show some alterations in their function among <i>S. lycopersicum</i> super strain B, and other species. |
| first_indexed | 2024-03-09T20:25:59Z |
| format | Article |
| id | doaj.art-3187865e55db4f0fba3b0216f2744000 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T20:25:59Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-3187865e55db4f0fba3b0216f27440002023-11-23T23:35:57ZengMDPI AGPlants2223-77472022-02-0111564110.3390/plants11050641Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain BHassan S. Al-Zahrani0Tarek A. A. Moussa1Hameed Alsamadany2Rehab M. Hafez3Michael P. Fuller4Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaBiological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaBiological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaBotany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, EgyptSchool of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UKThis investigation involved a comparative analysis of the small GTPase superfamily in <i>S. lycopersicum</i> super strain B compared to their analogues in leguminous and other non-leguminous species. The small GTPases superfamily members were recognized by tBLASTn searches. The sequences of amino acid were aligned using Clustal Omega and the analysis of phylogeny was performed with the MEGA7 package. Protein alignments were applied for all studied species. Three-dimensional models of RABA2, ROP9, and ROP10 from <i>Solanum lycopersicum</i> “Super strain B” were performed. The levels of mRNA of the Rab, Arf, Rop, and Ran subfamilies were detected in aerial tissues vs. roots. Significant divergences were found in the number of members and groups comprising each subfamily of the small GTPases and <i>Glycine max</i> had the highest count. High expression of Rab and Arf proteins was shown in the roots of legumes whilst in non-legume plants, the highest values were recorded in aerial tissues. <i>S. lycopersicum</i> super strain B had the highest expression of Rab and Arf proteins in its aerial tissues, which may indicate that diazotroph strains have supreme activities in the aerial tissues of strain B and act as associated N-fixing bacteria. The phylogenies of the small GTPase superfamily of the studied plants did not reveal asymmetric evolution of the Ra, Arf, Rop, and Ran subfamilies. Multiple sequence alignments derived from each of the Rab, Arf, and Rop proteins of <i>S. lycopersicum</i> super strain B showed a low frequency of substitutions in their domains. GTPases superfamily members have definite functions during infection, delivery, and maintenance of N<sub>2</sub>-fixing diazotroph but show some alterations in their function among <i>S. lycopersicum</i> super strain B, and other species.https://www.mdpi.com/2223-7747/11/5/641<i>S. lycopersicum</i> super strain Bphylogenetic analysesprotein expressionprotein sequence alignmentsmall GTPase superfamily |
| spellingShingle | Hassan S. Al-Zahrani Tarek A. A. Moussa Hameed Alsamadany Rehab M. Hafez Michael P. Fuller Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B Plants <i>S. lycopersicum</i> super strain B phylogenetic analyses protein expression protein sequence alignment small GTPase superfamily |
| title | Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B |
| title_full | Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B |
| title_fullStr | Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B |
| title_full_unstemmed | Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B |
| title_short | Phylogenetic and Expression Studies of Small GTP-Binding Proteins in <i>Solanum lycopersicum</i> Super Strain B |
| title_sort | phylogenetic and expression studies of small gtp binding proteins in i solanum lycopersicum i super strain b |
| topic | <i>S. lycopersicum</i> super strain B phylogenetic analyses protein expression protein sequence alignment small GTPase superfamily |
| url | https://www.mdpi.com/2223-7747/11/5/641 |
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