RNA-Binding S1 Domain in Bacterial, Archaeal and Eukaryotic Proteins as One of the Evolutionary Markers of Symbiogenesis
The RNA-binding S1 domain is a β-barrel with a highly conserved RNA-binding site on its surface. This domain is an important part of the structures of different bacterial, archaeal, and eukaryotic proteins. A distinctive feature of the S1 domain is multiple presences (structural repeats) in proteins...
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| Veröffentlicht in: | International journal of molecular sciences 2024-12, Vol.25 (23), p.13057 |
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| creator | Deryusheva, Evgenia I Machulin, Andrey V Surin, Alexey A Kravchenko, Sergey V Surin, Alexey K Galzitskaya, Oxana V |
| description | The RNA-binding S1 domain is a β-barrel with a highly conserved RNA-binding site on its surface. This domain is an important part of the structures of different bacterial, archaeal, and eukaryotic proteins. A distinctive feature of the S1 domain is multiple presences (structural repeats) in proteins and protein complexes. Here, we have analyzed all available protein sequences in the UniProt database to obtain data on the distribution of bacterial, eukaryotic and archaeal proteins containing the S1 domain. Mainly, the S1 domain is found in bacterial proteins with the number of domains varying from one to eight. Eukaryotic proteins contain from one to fifteen S1 domains, while in archaeal proteins, only one S1 domain is identified. Analysis of eukaryotic proteins containing S1 domains revealed a group of chloroplast S1 ribosomal proteins (ChRpS1) with characteristic properties of bacterial S1 ribosomal proteins (RpS1) from the Cyanobacteria. Also, in a separate group, chloroplast and mitochondrial elongation factor Ts containing two S1 structural domains were assigned. For mitochondrial elongation factor Ts, the features of S1 in comparison with the RpS1 from Cyanobacteria phylum and the Alphaproteobacteria class were revealed. The data obtained allow us to consider the S1 domain as one of the evolutionary markers of the symbiogenesis of bacterial and eukaryotic organisms. |
| doi_str_mv | 10.3390/ijms252313057 |
| format | Article |
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This domain is an important part of the structures of different bacterial, archaeal, and eukaryotic proteins. A distinctive feature of the S1 domain is multiple presences (structural repeats) in proteins and protein complexes. Here, we have analyzed all available protein sequences in the UniProt database to obtain data on the distribution of bacterial, eukaryotic and archaeal proteins containing the S1 domain. Mainly, the S1 domain is found in bacterial proteins with the number of domains varying from one to eight. Eukaryotic proteins contain from one to fifteen S1 domains, while in archaeal proteins, only one S1 domain is identified. Analysis of eukaryotic proteins containing S1 domains revealed a group of chloroplast S1 ribosomal proteins (ChRpS1) with characteristic properties of bacterial S1 ribosomal proteins (RpS1) from the Cyanobacteria. Also, in a separate group, chloroplast and mitochondrial elongation factor Ts containing two S1 structural domains were assigned. For mitochondrial elongation factor Ts, the features of S1 in comparison with the RpS1 from Cyanobacteria phylum and the Alphaproteobacteria class were revealed. The data obtained allow us to consider the S1 domain as one of the evolutionary markers of the symbiogenesis of bacterial and eukaryotic organisms.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms252313057</identifier><identifier>PMID: 39684768</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Amino Acid Sequence ; Amino acids ; Analysis ; Archaea - genetics ; Archaea - metabolism ; Archaeal Proteins - chemistry ; Archaeal Proteins - genetics ; Archaeal Proteins - metabolism ; Bacteria ; Bacteria - genetics ; Bacteria - metabolism ; Bacterial proteins ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biosynthesis ; Chloroplasts ; Cyanobacteria ; Eukaryota - genetics ; Eukaryota - metabolism ; Evolution, Molecular ; Ligands ; Phylogeny ; Plastids ; Protein Domains ; Ribonucleic acid ; Ribosomal Proteins - chemistry ; Ribosomal Proteins - genetics ; Ribosomal Proteins - metabolism ; RNA ; RNA polymerase ; Symbiosis - genetics ; Transcription factors</subject><ispartof>International journal of molecular sciences, 2024-12, Vol.25 (23), p.13057</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). 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For mitochondrial elongation factor Ts, the features of S1 in comparison with the RpS1 from Cyanobacteria phylum and the Alphaproteobacteria class were revealed. The data obtained allow us to consider the S1 domain as one of the evolutionary markers of the symbiogenesis of bacterial and eukaryotic organisms.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Archaea - genetics</subject><subject>Archaea - metabolism</subject><subject>Archaeal Proteins - chemistry</subject><subject>Archaeal Proteins - genetics</subject><subject>Archaeal Proteins - metabolism</subject><subject>Bacteria</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Bacterial proteins</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biosynthesis</subject><subject>Chloroplasts</subject><subject>Cyanobacteria</subject><subject>Eukaryota - genetics</subject><subject>Eukaryota - metabolism</subject><subject>Evolution, Molecular</subject><subject>Ligands</subject><subject>Phylogeny</subject><subject>Plastids</subject><subject>Protein Domains</subject><subject>Ribonucleic acid</subject><subject>Ribosomal Proteins - chemistry</subject><subject>Ribosomal Proteins - genetics</subject><subject>Ribosomal Proteins - metabolism</subject><subject>RNA</subject><subject>RNA polymerase</subject><subject>Symbiosis - genetics</subject><subject>Transcription factors</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptkUtP3TAQha2KildZdosssWFBqF95eHmBS6kEpSrtOpo4k4sviQ12guDf11dAKagaS2PZ3zkazSHkM2eHUmr2xS6HKHIhuWR5-YFsciVExlhRrv1z3yBbMS4ZE1Lkep1sSF1UqiyqTfLw8_ssO7KutW5Brzg98QNYR9M5AjNisNAf0Fkw14DQU3AtnU83EB79aA39EfyI1kUKkV46pL6j4zXS-b3vp9F6lzh6AeEGQ1z9XT0OjfULdBht_EQ-dtBH3Hnu2-T36fzX8Vl2fvn12_HsPDOiVGPWVbkogDMUBWsEatHlJTNojMq5MqYBw4VWneKVwhaBC1k0ZdPIXEkDSSG3yf6T723wdxPGsR5sNNj34NBPsZZcFZorJcuE7r1Dl34KLk23ohTXaX3VK7WAHmvrOj8GMCvTelZxrXPOVJGow_9QqVocrPEOO5ve3wiyJ4EJPsaAXX0b7JA2WHNWr5Ku3ySd-N3nYadmwPYv_RKt_AOEUqHq</recordid><startdate>20241201</startdate><enddate>20241201</enddate><creator>Deryusheva, Evgenia I</creator><creator>Machulin, Andrey V</creator><creator>Surin, Alexey A</creator><creator>Kravchenko, Sergey V</creator><creator>Surin, Alexey K</creator><creator>Galzitskaya, Oxana V</creator><general>MDPI AG</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3962-1520</orcidid><orcidid>https://orcid.org/0000-0001-9246-7369</orcidid><orcidid>https://orcid.org/0000-0002-4859-7219</orcidid><orcidid>https://orcid.org/0000-0002-1261-7919</orcidid></search><sort><creationdate>20241201</creationdate><title>RNA-Binding S1 Domain in Bacterial, Archaeal and Eukaryotic Proteins as One of the Evolutionary Markers of Symbiogenesis</title><author>Deryusheva, Evgenia I ; 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This domain is an important part of the structures of different bacterial, archaeal, and eukaryotic proteins. A distinctive feature of the S1 domain is multiple presences (structural repeats) in proteins and protein complexes. Here, we have analyzed all available protein sequences in the UniProt database to obtain data on the distribution of bacterial, eukaryotic and archaeal proteins containing the S1 domain. Mainly, the S1 domain is found in bacterial proteins with the number of domains varying from one to eight. Eukaryotic proteins contain from one to fifteen S1 domains, while in archaeal proteins, only one S1 domain is identified. Analysis of eukaryotic proteins containing S1 domains revealed a group of chloroplast S1 ribosomal proteins (ChRpS1) with characteristic properties of bacterial S1 ribosomal proteins (RpS1) from the Cyanobacteria. Also, in a separate group, chloroplast and mitochondrial elongation factor Ts containing two S1 structural domains were assigned. For mitochondrial elongation factor Ts, the features of S1 in comparison with the RpS1 from Cyanobacteria phylum and the Alphaproteobacteria class were revealed. The data obtained allow us to consider the S1 domain as one of the evolutionary markers of the symbiogenesis of bacterial and eukaryotic organisms.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39684768</pmid><doi>10.3390/ijms252313057</doi><orcidid>https://orcid.org/0000-0002-3962-1520</orcidid><orcidid>https://orcid.org/0000-0001-9246-7369</orcidid><orcidid>https://orcid.org/0000-0002-4859-7219</orcidid><orcidid>https://orcid.org/0000-0002-1261-7919</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Amino acids Analysis Archaea - genetics Archaea - metabolism Archaeal Proteins - chemistry Archaeal Proteins - genetics Archaeal Proteins - metabolism Bacteria Bacteria - genetics Bacteria - metabolism Bacterial proteins Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Biosynthesis Chloroplasts Cyanobacteria Eukaryota - genetics Eukaryota - metabolism Evolution, Molecular Ligands Phylogeny Plastids Protein Domains Ribonucleic acid Ribosomal Proteins - chemistry Ribosomal Proteins - genetics Ribosomal Proteins - metabolism RNA RNA polymerase Symbiosis - genetics Transcription factors |
| title | RNA-Binding S1 Domain in Bacterial, Archaeal and Eukaryotic Proteins as One of the Evolutionary Markers of Symbiogenesis |
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