«Previous Article|Table of Contents|Next Article»

¡¶´ó¶¹¿Æѧ¡·[ISSN:1000-9841/CN:23-1227/S]

Issue:

2021Äê02ÆÚ

Page:

177-185

Research Field:

Publishing date:

Info

Title:

Bioinformatic Analysis of PPR Gene Family in Soybean

Author(s):

PENG Shi-qiao;  LU Meng-dan;  YANG Meng-qi;  LI Jia-wen;  YUE Yan-lei

(College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China)

Keywords:

Soybean;  PPR gene family;  Bioinformatic analysis;  Evolution;  Phylogenetic analysis;  Tissue specificity expression

PACS:

-

DOI:

10.11861/j.issn.1000-9841.2021.02.0177

Abstract:

In order to find out soybean PPR genes and figure out the chromosomal distribution, the conserved domains, the subgrouping, the phylogenetic relationship and the expression characteristics of these genes, this study found 631 PPR genes through screening the soybean reference genome with the PPR model in the Pfam database. Clustering analysis was further performed to divide them into different subfamily with the softwares of MEME, ExPASy, TBtools and FigTree. The phylogenetic relationship and conserved domains of these subfamilies were also analyzed. We selected the representative genes from these subfamilies, and further evaluated their isoelectric points, UTR, CDS, and gene expression patterns. The results showed that, soybean PPR gene family could be divided into five subfamilies, DYW-, P-, PLS-, E/E+ and an unknown subfamily. Of them, DYW-subfamily was the biggest one, accounting for 57.2% of total soybean PPR genes. These subfamilies distributed unevenly in chromosomes, and their intron numbers varied greatly. DYW-subfamily contained fewer introns but contained more conserved motifs with two characteristical motifs of Motif7 and Motif4 locating in the C terminal. The representative genes of these subfamilies had a similar expression pattern with a high expression level in leaf but a low expression level in flower, root and stem. The UTR was missing in some members of these subfamilies. Glyma.19G095500, Glyma.11G086900, Glyma.02G175900 and Glyma.01G158100 were subgrouped into a new subgroup containing a unique motif of Motif8.

References:

£Û1£ÝBarkan A, Walker M, Nolasco M, et al. A nuclear mutation in maize blocks the processing and translation of several chloroplast mRNAs and provides evidence for the differential translation of alternative mRNA forms£ÛJ£Ý. EMBO Journal, 1994, 13(13): 3170-3181.£Û2£ÝSmall I D, Peeters N. The PPR motif-A TPR-related motif prevalent in plant organellar proteins£ÛJ£Ý. Trends in Biochemical Science, 2000, 25(2): 45-47.£Û3£ÝHayes M L, Santibanez P I. A plant pentatricopeptide repeat protein with a DYW-deaminase domain is sufficient for catalyzing C-to-U RNA editing ª«in vitroª«£ÛJ£Ý. Journal of Biological Chemistry, 2020, 295(11): 3497-3505.£Û4£ÝOldenkott B, Yang Y, Lesch E, et al. Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in ª«Escherichia coliª«£ÛJ£Ý. Communications Biology, 2019, 2(1): 85.£Û5£Ý¶¡°²Ã÷, ÀîÁè, ÇüÐñ, µÈ. ·¬ÇÑPPR»ùÒò¼Ò×åµÄ¼ø¶¨ÓëÉúÎïÐÅϢѧ·ÖÎö£ÛJ£Ý. ÒÅ´«, 2014, 36(1): 77-84. (Ding A M, Li L, Qu X, et al. Identification and bioinformatics analysis of PPR gene family in Tomato£ÛJ£Ý. Hereditas, 2014, 36(1): 77-84.)£Û6£ÝO¡äToole N, Hattori M, Andres C, et al. On the expansion of the pentatricopeptide repeat gene family in plants£ÛJ£Ý. Molecular Biology and Evolution, 2008, 25(6): 1120-1128.£Û7£Ý½Ƽ, Óá¼ÎÄþ. PPRµ°°×Ó°ÏìÖ²ÎïÉú³¤·¢ÓýµÄÑо¿½øÕ¹£ÛJ£Ý. Ö²ÎïÉúÀíѧ±¨, 2013, 49(10): 989-999. (Lu P, Yu J N. Research Progress on the effect of PPR protein on plant growth and development£ÛJ£Ý. Plant Physiology Journal, 2003, 49(10):989-999.)£Û8£Ý¶¡°²Ã÷, ÇüÐñ, ËïÓñºÏ. Ö²ÎïPPRµ°°×¼Ò×åÑо¿½øÕ¹£ÛJ£Ý. Öйúũѧͨ±¨, 2014, 30(9): 218-224.(Ding A M, Qu X, Sun H Y. Research progress of plant PPR protein£ÛJ£Ý. Chinese Agricultural Science Bulletin, 2014, 30(9): 218-224.)£Û9£ÝChen G L, Zou Y, Hu J H, et al. Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments£ÛJ£Ý. BMC Genomics, 2018, 19(1): 720.£Û10£ÝLurin C, Andr¨¦s C, Aubourg S, et al. Genome-wide analysis of ª«Arabidopsis ª«pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis£ÛJ£Ý. Plant Cell, 2004, 16(8): 2089-2103.£Û11£ÝLiu J M, Xu Z S, Lu P P, et al. Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet£ÛJ£Ý. BMC Genomics, 2016, 17(1): 840.£Û12£ÝTakenaka M, Verbitskiy D, Zehrmann A, et al. Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of ª«Arabidopsis thalianaª«£ÛJ£Ý. Journal of Biological Chemistry, 2010, 285(35): 27122-27129.£Û13£ÝZamudio-Ochoa A, Camacho-Villasana Y, Garc¨ªa-Guerrero A E, et al. The Pet309 pentatricopeptide repeat motifs mediate efficient binding to the mitochondrial COX1 transcript in yeast£ÛJ£Ý. RNA Biology, 2014, 11(7): 953-967.£Û14£ÝCoffin J W, Dhillon R, Ritzel R G, et al. The Neurospora crassa cya-5 nuclear gene encodes a protein with a region of homology to the ª«Saccharomyces cerevisiaeª« PET309 protein and is required in a post-transcriptional step for the expression of the mitochondrially encoded COXI protein£ÛJ£Ý. Current Genetics, 1997, 32(4): 273-280.£Û15£ÝTasaka M, Shikanai T, Kotera E. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts£ÛJ£Ý. Nature, 2005, 433(7023): 326-330.£Û16£ÝDas A K. The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions£ÛJ£Ý. EMBO Journal, 1998, 17(5): 1192-1199.£Û17£ÝOguchi T, Sage-Ono K, Kamada H, et al. Genomic structure of a novel ª«Arabidopsisª« clock-controlled gene, AtC401, which encodes a pentatricopeptide repeat protein£ÛJ£Ý. Gene, 2004, 330: 29-37.£Û18£ÝOguchi T, Sage-Ono K, Kamada H, et al. Characterization of transcriptional oscillation of an ª«Arabidopsisª« homolog of PnC401 related to photoperiodic induction of flowering in ª«Pharbitis nilª«£ÛJ£Ý. Plant and Cell Physiology, 2004, 45(2): 232-235.£Û19£ÝAlfonso A A, Bentolila S, Hanson M R. Evaluation of the fertility restoring ability of Rf-PPR592 in petunia£ÛJ£Ý. Philippine Agricultural Scientist, 2003, 86(3): 303-315.£Û20£ÝMora J R H, Rivals E, Mireau H, et al. Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)£ÛJ£Ý. BMC Plant Biology, 2010, 10(1): 35-35.£Û21£ÝKazama T, Nakamura T, Watanabe M, et al. Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice£ÛJ£Ý. Plant Journal, 2008, 55(4): 619-628.£Û22£ÝCushing D A, Forsthoefel N R, Gestaut D R, et al. Arabidopsis emb175 and other ª«pprª« knockout mutants reveal essential roles for pentatricopeptide repeat (PPR) proteins in plant embryogenesis£ÛJ£Ý. Planta, 2005, 221(3): 424-436.£Û23£ÝÇñºì÷, ÀúÖ¾, ÓÚåû, µÈ. »ùÓÚÔª·ÖÎöµÄ´ó¶¹º¬Áò°±»ùËáÏà¹Ø»ùÒòÍÚ¾òÓëÐÅϢѧ·ÖÎö£ÛJ£Ý. ÖйúÓÍÁÏ×÷Îïѧ±¨, 2015, 37(2): 141-147. (Qiu H M, Li Z, Yu Y, et al. Mining and analysis of genes related to sulfur-containing amino acids in soybean based on Meta-QTL £ÛJ£Ý. Chinese Journal of oil crops, 2015, 37(2): 141-147.)£Û24£ÝSong Q X, Liu Y F, Hu X Y, et al. Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing £ÛJ£Ý. BMC Plant Biology, 2011, 11: 5.£Û25£ÝÕÔ·å. ´ó¶¹ª«GmZTLª«»ùÒòµÄ¹¦ÄÜÑо¿£ÛD£Ý. ¹óÖÝ: ¹óÖÝ´óѧ, 2008: 42. (Zhao F. Research on the function of soybean gene ª«GmZTLª«£ÛD£Ý. Guizhou:Guizhou University, 2008: 42.)£Û26£ÝÀî´Ô´Ô. ´ó¶¹Çú¾¥ºÍ±â¾¥ÐÔ×´»ùÒòµÄ¾«Ï¸¶¨Î»ÓëºòÑ¡»ùÒò·ÖÎö£ÛD£Ý. ÄϾ©: ÄϾ©Å©Òµ´óѧ, 2011: 38. (Li C C. Fine mapping and candidate gene exploration of loci corresponding to brachytic and fasciation stem in soybean£ÛD£Ý. Nanjing:Nanjing Agricultural University, 2011: 38.)£Û27£ÝFinn R D, Mistry J, Schuster-Bockler B, et al. Pfam: Clans, web tools and services£ÛJ£Ý. Nucleic Acids Research, 2006, 34: 247-251.£Û28£ÝTamura K, Peterson D, Peterson N, et al.MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods£ÛJ£Ý. Molecular and Biology Evolution, 2011, 28(10): 2731-2739.£Û29£ÝChen C, Chen H, Zhang Y, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data£ÛJ£Ý. Molecular Plant, 2020, 13(8): 1194-1202.£Û30£ÝËÎѧ»¨. Ö²ÎïPPR»ùÒò¼Ò×åµÄ¼ø¶¨Óë½ø»¯·ÖÎö£ÛD£Ý. ¹ãÖÝ£º»ªÄÏÀí¹¤´óѧ, 2017. (Song X H. Identification and evolution of pentatricopeptide repeat gene family in plants£ÛD£Ý. Guangzhou: South China University of Technology, 2017.)£Û31£ÝLecharny A, Boudet N, Gy I, et al. Introns in, introns out in plant gene families: A genomic approach of the dynamics of gene structure£ÛJ£Ý. Journal of Structural and Functional Genomics, 2003, 3(1-4): 111-116.

Memo

Memo:

-

Common functions

Last Update: 2021-07-19