Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program
Glycine- and arginine-rich (GAR) motifs with different combinations of RG/RGG repeats are present in many proteins. The nucleolar rRNA 2′-O-methyltransferase fibrillarin (FBL) contains a conserved long N-terminal GAR domain with more than 10 RGG plus RG repeats separated by specific amino acids, mos...
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MDPI AG
2023-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/2/330 |
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| author | Yi-Chun Wang Shang-Hsuan Huang Chien-Ping Chang Chuan Li |
| author_facet | Yi-Chun Wang Shang-Hsuan Huang Chien-Ping Chang Chuan Li |
| author_sort | Yi-Chun Wang |
| collection | DOAJ |
| description | Glycine- and arginine-rich (GAR) motifs with different combinations of RG/RGG repeats are present in many proteins. The nucleolar rRNA 2′-O-methyltransferase fibrillarin (FBL) contains a conserved long N-terminal GAR domain with more than 10 RGG plus RG repeats separated by specific amino acids, mostly phenylanalines. We developed a GAR motif finder (GMF) program based on the features of the GAR domain of FBL. The G(0,3)-X(0,1)-R-G(1,2)-X(0,5)-G(0,2)-X(0,1)-R-G(1,2) pattern allows the accommodation of extra-long GAR motifs with continuous RG/RGG interrupted by polyglycine or other amino acids. The program has a graphic interface and can easily output the results as .csv and .txt files. We used GMF to show the characteristics of the long GAR domains in FBL and two other nucleolar proteins, nucleolin and GAR1. GMF analyses can illustrate the similarities and also differences between the long GAR domains in the three nucleolar proteins and motifs in other typical RG/RGG-repeat-containing proteins, specifically the FET family members FUS, EWS, and TAF15 in position, motif length, RG/RGG number, and amino acid composition. We also used GMF to analyze the human proteome and focused on the ones with at least 10 RGG plus RG repeats. We showed the classification of the long GAR motifs and their putative correlation with protein/RNA interactions and liquid–liquid phase separation. The GMF algorithm can facilitate further systematic analyses of the GAR motifs in proteins and proteomes. |
| first_indexed | 2024-03-11T08:47:24Z |
| format | Article |
| id | doaj.art-e490427f36c44822bdcec6055cc2df23 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T08:47:24Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-e490427f36c44822bdcec6055cc2df232023-11-16T20:41:28ZengMDPI AGGenes2073-44252023-01-0114233010.3390/genes14020330Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder ProgramYi-Chun Wang0Shang-Hsuan Huang1Chien-Ping Chang2Chuan Li3Department of Biomedical Sciences, Chung Shan Medical University, Taichung 40201, TaiwanDepartment of Biomedical Sciences, Chung Shan Medical University, Taichung 40201, TaiwanDepartment of Biomedical Sciences, Chung Shan Medical University, Taichung 40201, TaiwanDepartment of Biomedical Sciences, Chung Shan Medical University, Taichung 40201, TaiwanGlycine- and arginine-rich (GAR) motifs with different combinations of RG/RGG repeats are present in many proteins. The nucleolar rRNA 2′-O-methyltransferase fibrillarin (FBL) contains a conserved long N-terminal GAR domain with more than 10 RGG plus RG repeats separated by specific amino acids, mostly phenylanalines. We developed a GAR motif finder (GMF) program based on the features of the GAR domain of FBL. The G(0,3)-X(0,1)-R-G(1,2)-X(0,5)-G(0,2)-X(0,1)-R-G(1,2) pattern allows the accommodation of extra-long GAR motifs with continuous RG/RGG interrupted by polyglycine or other amino acids. The program has a graphic interface and can easily output the results as .csv and .txt files. We used GMF to show the characteristics of the long GAR domains in FBL and two other nucleolar proteins, nucleolin and GAR1. GMF analyses can illustrate the similarities and also differences between the long GAR domains in the three nucleolar proteins and motifs in other typical RG/RGG-repeat-containing proteins, specifically the FET family members FUS, EWS, and TAF15 in position, motif length, RG/RGG number, and amino acid composition. We also used GMF to analyze the human proteome and focused on the ones with at least 10 RGG plus RG repeats. We showed the classification of the long GAR motifs and their putative correlation with protein/RNA interactions and liquid–liquid phase separation. The GMF algorithm can facilitate further systematic analyses of the GAR motifs in proteins and proteomes.https://www.mdpi.com/2073-4425/14/2/330fibrillarinGAR1glycine- and arginine-rich (GAR) motifsGAR motif finder (GMF)RG/RGG repeat-containing proteinsarginine methylation |
| spellingShingle | Yi-Chun Wang Shang-Hsuan Huang Chien-Ping Chang Chuan Li Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program Genes fibrillarin GAR1 glycine- and arginine-rich (GAR) motifs GAR motif finder (GMF) RG/RGG repeat-containing proteins arginine methylation |
| title | Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program |
| title_full | Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program |
| title_fullStr | Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program |
| title_full_unstemmed | Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program |
| title_short | Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program |
| title_sort | identification and characterization of glycine and arginine rich motifs in proteins by a novel gar motif finder program |
| topic | fibrillarin GAR1 glycine- and arginine-rich (GAR) motifs GAR motif finder (GMF) RG/RGG repeat-containing proteins arginine methylation |
| url | https://www.mdpi.com/2073-4425/14/2/330 |
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