Genome‐wide identification, evolution, and expression analysis of RNA‐binding glycine‐rich protein family in maize

Zhang, Jianhua; Zhao, Yanxin; Xiao, Hailin; Zheng, Yanyan; Yue, Bing

doi:10.1111/jipb.12210

Cited by 26 publications

(46 citation statements)

References 47 publications

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“…The remaining 14 proteins (IVa = 6; IVb = 2; IVc = 2; IVd = 4) were selected to represent the OsRBG class (Table S3). Twenty-three RBGs (IVa = 6; IVb = 6; IVc = 2; IVd = 9) were previously identified in the maize genome by whole-genome sequence analysis (Zhang et al 2014). Relying on the results of Zhang et al (2014), we did not screen the maize whole genome; instead, we performed an ortholog search of RGAP and POG databases using the 23 ZmRBGs.…”

Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

“…Twenty-three RBGs (IVa = 6; IVb = 6; IVc = 2; IVd = 9) were previously identified in the maize genome by whole-genome sequence analysis (Zhang et al 2014). Relying on the results of Zhang et al (2014), we did not screen the maize whole genome; instead, we performed an ortholog search of RGAP and POG databases using the 23 ZmRBGs. This search indicated that the orthologs of U11/U12-31 K (GRMZM2G053223), TBP-associated factor 15B (TAF15B; GRMZM2G097775), UBP1-associated protein 2 (UBA2; GRMZM2G132465) and nucleolin-like (GRMZM2G001850 and GRMZM2G131943) proteins were included in the ZmRBG class.…”

Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

“…Our ortholog search identified two additional ZmRBG members, GRMZM2G009448 and GRMZM2G050218. GRMZM2G050218 was mistakenly recognized as a 30 K-RRM protein by Zhang et al (2014), with no information reported for GRMZM2G009448. In addition, GRMZM6G285883 was identified as a paralog to GRMZM2G082931 but was lacking its N-terminal RRM domain; we excluded this protein.…”

Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

“…The number of IVd members in both Arabidopsis and rice is currently unknown. Zhang et al (2014) recently screened the wholegenome sequence of maize (Zea mays) and revealed that more RBGs (IVa = 6; IVb = 6; IVc = 2; IVd = 9) are present in maize than in Arabidopsis and rice. In their study, RBGs were defined as proteins containing >50 % glycine residues within any 20 amino acids in the peptide sequence in addition to a RRM/CSD domain with or without C 2 HCtype ZnFs.…”

Section: Introductionmentioning

confidence: 99%

“…From this perspective, the RBGs of Arabidopsis (AtRBG), rice (OsRBG) and maize (ZmRBG) must be re-evaluated. In addition, the presence of IVd members in sugarcane (Saccharum officinarum) (Fusaro et al 2001), Eucalyptus (Bocca et al 2005) and maize (Zhang et al 2014) suggests that IVd members remain to be discovered in Arabidopsis and rice. To obtain complete information about RBGs of Arabidopsis and rice, analysis of their corresponding genomes is therefore essential.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

et al. 2015

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RNA-binding glycine-rich (RBG) proteins play diverse roles in plant growth, development, protection and genome organization. An overly broad definition for class IV glycine-rich proteins (GRPs), namely RNA-binding activity and a glycine-rich C-terminus, has resulted in many distantly related and/or non-related proteins being grouped into this class of RBGs. This definition has hampered the study of RBG evolution. In this study, we used a comparative genomic approach consisting of ortholog, homolog, synteny and phylogenetic analyses to legitimately exclude all distantly/non-related proteins from class IV GRPs and to identify 15, 22, 12 and 18 RBG proteins in Arabidopsis, Chinese cabbage, rice and maize genomes, respectively. All identified RBGs could be divided into three subclasses, namely RBGA, RBGB and RBGD, which may be derived from a common ancestor. We assigned RBGs excluded from class IV GRPs to a separate RBG superfamily. RBGs have evolved and diversified in different species via different mechanisms; segmental duplication and recombination have had major effects, with tandem duplication, intron addition/deletion and domain recombination/deletion playing minor roles. Loss and retention of duplicated RBGs after polyploidization has been species and subclass specific. For example, following recent whole-genome duplication and triplication in maize and Chinese cabbage, respectively, most duplicated copies of RBGA have been lost in maize while RBGD duplicates have been retained; in Chinese cabbage, in contrast, RBGA duplicates have been retained while RBGD duplicates have been lost. Our findings reveal fundamental information and shed new light on the structural characteristics and evolutionary dynamics of RBGs.

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Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

Section: Genome-wide Identification Selection Classification and Namentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

et al. 2015

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Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

2015

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This study focused on the identification and phylogenetic analysis of glycine-rich RNA binding proteins that contain an RNA recognition motif (RRM)-type RNA binding domain in addition to a region with contiguous glycine residues in representative plant species. In higher plants, glycine-rich proteins with an RRM have met considerable interest as they are responsive to environmental cues and play a role in cold tolerance, pathogen defense, flowering time control, and circadian timekeeping. To identify such RRM containing proteins in plant genomes we developed an RRM profile based on the known glycine-rich RRM containing proteins in the reference plant Arabidopsis thaliana. The application of this remodeled RRM profile that omitted sequences from non-plant species reduced the noise when searching plant genomes for RRM proteins compared to a search performed with the known RRM_1 profile. Furthermore, we developed an island scoring function to identify regions with contiguous glycine residues, using a sliding window approach. This approach tags regions in a protein sequence with a high content of the same amino acid, and repetitive structures score higher. This definition of repetitive structures in a fixed sequence length provided a new glance for characterizing patterns which cannot be easily described as regular expressions. By combining the profile-based domain search for well-conserved regions (the RRM) with a scoring technique for regions with repetitive residues we identified groups of proteins related to the A. thaliana glycine-rich RNA binding proteins in eight plant species.

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Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera)

Tang

Huang

et al. 2021

Physiol Mol Biol Plants

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Genome‐wide identification, evolution, and expression analysis of RNA‐binding glycine‐rich protein family in maize

Cited by 26 publications

References 47 publications

Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera)

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