Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida
Abstract Background SET is a conserved protein domain with methyltransferase activity. Several genome and transcriptome data in plant lineage (Archaeplastida) are available but status of SET domain proteins in most of the plant lineage is not comprehensively analysed. Results In this study phylogeny...
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| Format: | Article |
| Language: | English |
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BMC
2017-12-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-017-1177-1 |
| _version_ | 1819076143323545600 |
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| author | Supriya Sarma Mukesh Lodha |
| author_facet | Supriya Sarma Mukesh Lodha |
| author_sort | Supriya Sarma |
| collection | DOAJ |
| description | Abstract Background SET is a conserved protein domain with methyltransferase activity. Several genome and transcriptome data in plant lineage (Archaeplastida) are available but status of SET domain proteins in most of the plant lineage is not comprehensively analysed. Results In this study phylogeny and domain organisation of 506 computationally identified SET domain proteins from 16 members of plant lineage (Archaeplastida) are presented. SET domain proteins of rice and Arabidopsis are used as references. This analysis revealed conserved as well as unique features of SET domain proteins in Archaeplastida. SET domain proteins of plant lineage can be categorised into five classes- E(z), Ash, Trx, Su(var) and Orphan. Orphan class of SET proteins contain unique domains predominantly in early Archaeplastida. Contrary to previous study, this study shows first appearance of several domains like SRA on SET domain proteins in chlorophyta instead of bryophyta. Conclusion The present study is a framework to experimentally characterize SET domain proteins in plant lineage. |
| first_indexed | 2024-12-21T18:36:37Z |
| format | Article |
| id | doaj.art-3d47cfe9eb3749ebb86f0647aeb833df |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T18:36:37Z |
| publishDate | 2017-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-3d47cfe9eb3749ebb86f0647aeb833df2022-12-21T18:54:07ZengBMCBMC Plant Biology1471-22292017-12-0117111210.1186/s12870-017-1177-1Phylogenetic relationship and domain organisation of SET domain proteins of ArchaeplastidaSupriya Sarma0Mukesh Lodha1Centre for Cellular and Molecular Biology (CSIR)Centre for Cellular and Molecular Biology (CSIR)Abstract Background SET is a conserved protein domain with methyltransferase activity. Several genome and transcriptome data in plant lineage (Archaeplastida) are available but status of SET domain proteins in most of the plant lineage is not comprehensively analysed. Results In this study phylogeny and domain organisation of 506 computationally identified SET domain proteins from 16 members of plant lineage (Archaeplastida) are presented. SET domain proteins of rice and Arabidopsis are used as references. This analysis revealed conserved as well as unique features of SET domain proteins in Archaeplastida. SET domain proteins of plant lineage can be categorised into five classes- E(z), Ash, Trx, Su(var) and Orphan. Orphan class of SET proteins contain unique domains predominantly in early Archaeplastida. Contrary to previous study, this study shows first appearance of several domains like SRA on SET domain proteins in chlorophyta instead of bryophyta. Conclusion The present study is a framework to experimentally characterize SET domain proteins in plant lineage.http://link.springer.com/article/10.1186/s12870-017-1177-1ArchaeplastidaHistone modificationsEpigeneticsSET domainPolycombPhylogenetic analysis |
| spellingShingle | Supriya Sarma Mukesh Lodha Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida BMC Plant Biology Archaeplastida Histone modifications Epigenetics SET domain Polycomb Phylogenetic analysis |
| title | Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida |
| title_full | Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida |
| title_fullStr | Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida |
| title_full_unstemmed | Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida |
| title_short | Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida |
| title_sort | phylogenetic relationship and domain organisation of set domain proteins of archaeplastida |
| topic | Archaeplastida Histone modifications Epigenetics SET domain Polycomb Phylogenetic analysis |
| url | http://link.springer.com/article/10.1186/s12870-017-1177-1 |
| work_keys_str_mv | AT supriyasarma phylogeneticrelationshipanddomainorganisationofsetdomainproteinsofarchaeplastida AT mukeshlodha phylogeneticrelationshipanddomainorganisationofsetdomainproteinsofarchaeplastida |