Molecular characterization, expression pattern and function analysis of the rice <i>OsDUF866</i> family

Li, Lihua; Xie, Chen; Ye, Taozhi; Xu, Jin-Quan; Chen, Rongjun; Gao, Xiaoling; Zhu, Jianqing; Xu, Zhengjun

doi:10.1080/13102818.2016.1268932

Cited by 15 publications

(25 citation statements)

References 35 publications

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“…Although there have been numerous reports on other gene families in plants, there have been few reports of comprehensive genomic analyses of DUF families. Such analyses have been reported for DUF221, DUF810, DUF866, DUF936 and DUF1618 from Oryza sativa [8][9][10][11][12], the DUF481 and DUF724 gene families from Arabidopsis thaliana [13,14], and DUF1313 genes from 81 photoautotrophic species [6].…”

Section: Introductionsupporting

confidence: 52%

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses

et al. 2020

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Background: Domain of unknown function (DUF) proteins represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. The DUF4228 gene family is one of these families in plants that has not been described previously. Results: In this study, we performed an extensive comparative analysis of DUF4228 proteins and determined their phylogeny in the plant lineage. A total of 489 high-confidence DUF4228 family members were identified from 14 land plant species, which subdivided into three distinct phylogenetic groups: group I, group II and group III. A highly conserved DUF4228 domain and motif distribution existed in each group, implying their functional conservation. To reveal the possible biological functions of these DUF4228 genes, 25 ATDUF4228 sequences from Arabidopsis thaliana were selected for further analysis of characteristics such as their chromosomal position, gene duplications and gene structures. Ka/Ks analysis identified seven segmental duplication events, while no tandemly duplication gene pairs were found in A. thaliana. Some cis-elements responding to abiotic stress and phytohormones were identified in the upstream sequences of the ATDUF4228 genes. Expression profiling of the ATDUF4228 genes under abiotic stresses (mainly osmotic, salt and cold) and protein-protein interaction prediction suggested that some ATDUF4228 genes are may be involved in the pathways of plant resistance to abiotic stresses. Conclusion: These results expand our knowledge of the evolution of the DUF4228 gene family in plants and will contribute to the elucidation of the biological functions of DUF4228 genes in the future.

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Section: Introductionsupporting

confidence: 52%

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses

et al. 2020

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“…The rice genome includes 10 duplicated blocks accounting for 45% of its total size [34]. Therefore, it could be speculated that genome duplication might be the mechanism that underlies the distribution of OsDUF872 family members in different chromosomes, similar to that previously suggested for OsDUF866 family members and OsDUF946 family members [31,35].…”

Section: Identification Of Osduf872 Family Members In Ricesupporting

confidence: 52%

“…OsSIDP366, a DUF1644 gene, positively regulates the salt and drought resistance in rice [44]. In our previous study, OsDUF866.1 improved heat stress resistance [31] and OsDUF946.4 improved the tolerance to salt and drought in transgenic E. coli [35]. In this study, OsDUF872.2 improved the heat resistance in transgenic E. coli.…”

Section: Osduf8722 Improved Heat Resistance In Transgenic E Colimentioning

confidence: 59%

“…Next, the total RNA was treated with RNase-free DNase I (Invitrogen, Carlsbad, CA, USA) for 15 min to degrade any potential DNA contamination, and then used for first-strand cDNA synthesis. Real-time PCR was performed as described before [31]. The rice Actin1 gene (LOC ç Os03g50885) was used as an internal control with primers 5'-TGGCATCTCTCAG-CACATTC-3' and 5'-TGCACAATGGATGGGCCAGA-3'.…”

Section: Rna Extraction and Real-time Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

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Molecular characterisation and function analysis of the rice OsDUF872 family

et al. 2018

Biotechnology & Biotechnological Equipment

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With the advance of sequencing technology, the number of sequenced plant genomes has been rapidly increasing. However, many plant proteins in public databases are recognised as proteins with domains of unknown function (DUF). DUF872 is such a protein family that consists of plant proteins with unknown function. In this study, we analysed three DUF872 members (OsDUF872.1, OsDUF872.1 and OsDUF872.3) in rice Nipponbare with three distinct motifs. Real-time polymerase chain reaction showed that the expression patterns of the three corresponding OsDUF872 proteinencoding genes varied in 15 different rice tissues. The expression of OsDUF872.2 was significantly (P < 0.01) upregulated under salt, cold and heat stress conditions. Overexpression of OsDUF872.2 in Escherichia coli significantly improved the resistance to heat. These results improve our understanding of these poorly-studied proteins and provide information for future studies on other proteins of unknown function.

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“…The rice genome includes 10 duplicated blocks accounting for 45% of its total size [36]. Therefore, it could be speculated that genome duplication might be the mechanism that underlies the distribution of OsDUF946 family members in different chromosomes, similar to that previously suggested for OsDUF866 members [37].…”

Section: Identification Of Osduf946 Family Members In Ricementioning

confidence: 65%

Molecular characterization and function analysis of the rice OsDUF946 family

et al. 2017

Biotechnology & Biotechnological Equipment

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The domain of unknown function DUF946 family consists of plant proteins with an average length of around 239 residues that have no characterized function. The gene family needs deeper characterization and functional analysis of its members. In this study, we report five OsDUF946 (OsDUF946.1-OsDUF946.5) family members in rice Nipponbare with three distinct motifs. All the OsDUF946 proteins were classified into three major groups (I, II, III) by phylogenetic analysis. Realtime polymerase chain reaction showed that the expression patterns of the five OsDUF946 family members were different in 15 different rice tissues as well as under various stress conditions and abscisic acid treatment. The expression of OsDUF946.1 was significantly downregulated under salt, cold and heat stress, while the expression of OsDUF946.4 and OsDUF946.5 was significantly upregulated under drought and salt conditions. Overexpression of OsDUF946.4 in Escherichia coli significantly improved the resistance to salt and drought, while overexpression of OsDUF946.5 in E. coli did not have such an effect. The obtained results provide a starting point for further research into the function of the OsDUF946 family in rice.

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Molecular characterization, expression pattern and function analysis of the rice OsDUF866 family

Cited by 15 publications

References 35 publications

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses

Molecular characterisation and function analysis of the rice OsDUF872 family

Molecular characterization and function analysis of the rice OsDUF946 family

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