Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole
Indole synthase (INS), a homologous cytosolic enzyme of the plastidal tryptophan synthase A (TSA), has been reported as the first enzyme in the tryptophan-independent pathway of auxin synthesis. This suggestion was challenged as INS or its free indole product may interact with tryptophan synthase B...
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MDPI AG
2023-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/8/1687 |
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| author | Yousef M. Abu-Zaitoon Ezz Al-Dein Muhammed Al-Ramamneh Abdel Rahman Al Tawaha Sulaiman M. Alnaimat Fouad A. Almomani |
| author_facet | Yousef M. Abu-Zaitoon Ezz Al-Dein Muhammed Al-Ramamneh Abdel Rahman Al Tawaha Sulaiman M. Alnaimat Fouad A. Almomani |
| author_sort | Yousef M. Abu-Zaitoon |
| collection | DOAJ |
| description | Indole synthase (INS), a homologous cytosolic enzyme of the plastidal tryptophan synthase A (TSA), has been reported as the first enzyme in the tryptophan-independent pathway of auxin synthesis. This suggestion was challenged as INS or its free indole product may interact with tryptophan synthase B (TSB) and, therefore, with the tryptophan-dependent pathway. Thus, the main aim of this research was to find out whether INS is involved in the tryptophan-dependent or independent pathway. The gene coexpression approach is widely recognized as an efficient tool to uncover functionally related genes. Coexpression data presented here were supported by both RNAseq and microarray platforms and, hence, considered reliable. Coexpression meta-analyses of Arabidopsis genome was implemented to compare between the coexpression of <i>TSA</i> and <i>INS</i> with all genes involved in the production of tryptophan via the chorismate pathway. Tryptophan synthase A was found to be coexpressed strongly with <i>TSB1/2</i>, <i>anthranilate synthase A1/B1</i>, <i>phosphoribosyl anthranilate transferase1</i>, as well as <i>indole-3-glycerol phosphate synthase1</i>. However, <i>INS</i> was not found to be coexpressed with any target genes suggesting that it may exclusively and independently be involved in the tryptophan-independent pathway. Additionally, annotation of examined genes as ubiquitous or differentially expressed were described and subunits-encoded genes available for the assembly of tryptophan and anthranilate synthase complex were suggested. The most probable TSB subunits expected to interact with TSA is TSB1 then TSB2. Whereas TSB3 is only used under limited hormone conditions to assemble tryptophan synthase complex, putative TSB4 is not expected to be involved in the plastidial synthesis of tryptophan in Arabidopsis. |
| first_indexed | 2024-03-11T04:35:49Z |
| format | Article |
| id | doaj.art-29517befa8ff4bda9b68a31b02a0f64f |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T04:35:49Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-29517befa8ff4bda9b68a31b02a0f64f2023-11-17T21:00:13ZengMDPI AGPlants2223-77472023-04-01128168710.3390/plants12081687Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free IndoleYousef M. Abu-Zaitoon0Ezz Al-Dein Muhammed Al-Ramamneh1Abdel Rahman Al Tawaha2Sulaiman M. Alnaimat3Fouad A. Almomani4Department of Biology, Faculty of science, Al-Hussein Bin Talal University, Maan 71111, JordanDepartment of Agricultural Sciences, AL-Shouback University College, Al-Balqa Applied University, Maan 71911, JordanDepartment of Biology, Faculty of science, Al-Hussein Bin Talal University, Maan 71111, JordanDepartment of Biology, Faculty of science, Al-Hussein Bin Talal University, Maan 71111, JordanDepartment of Applied Biology, Jordan University of Science and Technology, Irbid 22110, JordanIndole synthase (INS), a homologous cytosolic enzyme of the plastidal tryptophan synthase A (TSA), has been reported as the first enzyme in the tryptophan-independent pathway of auxin synthesis. This suggestion was challenged as INS or its free indole product may interact with tryptophan synthase B (TSB) and, therefore, with the tryptophan-dependent pathway. Thus, the main aim of this research was to find out whether INS is involved in the tryptophan-dependent or independent pathway. The gene coexpression approach is widely recognized as an efficient tool to uncover functionally related genes. Coexpression data presented here were supported by both RNAseq and microarray platforms and, hence, considered reliable. Coexpression meta-analyses of Arabidopsis genome was implemented to compare between the coexpression of <i>TSA</i> and <i>INS</i> with all genes involved in the production of tryptophan via the chorismate pathway. Tryptophan synthase A was found to be coexpressed strongly with <i>TSB1/2</i>, <i>anthranilate synthase A1/B1</i>, <i>phosphoribosyl anthranilate transferase1</i>, as well as <i>indole-3-glycerol phosphate synthase1</i>. However, <i>INS</i> was not found to be coexpressed with any target genes suggesting that it may exclusively and independently be involved in the tryptophan-independent pathway. Additionally, annotation of examined genes as ubiquitous or differentially expressed were described and subunits-encoded genes available for the assembly of tryptophan and anthranilate synthase complex were suggested. The most probable TSB subunits expected to interact with TSA is TSB1 then TSB2. Whereas TSB3 is only used under limited hormone conditions to assemble tryptophan synthase complex, putative TSB4 is not expected to be involved in the plastidial synthesis of tryptophan in Arabidopsis.https://www.mdpi.com/2223-7747/12/8/1687indole synthasetryptophan synthase Atryptophan synthase Bcoexpressionlogit score |
| spellingShingle | Yousef M. Abu-Zaitoon Ezz Al-Dein Muhammed Al-Ramamneh Abdel Rahman Al Tawaha Sulaiman M. Alnaimat Fouad A. Almomani Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole Plants indole synthase tryptophan synthase A tryptophan synthase B coexpression logit score |
| title | Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole |
| title_full | Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole |
| title_fullStr | Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole |
| title_full_unstemmed | Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole |
| title_short | Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole |
| title_sort | comparative coexpression analysis of indole synthase and tryptophan synthase a reveals the independent production of auxin via the cytosolic free indole |
| topic | indole synthase tryptophan synthase A tryptophan synthase B coexpression logit score |
| url | https://www.mdpi.com/2223-7747/12/8/1687 |
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