scholarly journals Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mehtab Muhammad Aslam ◽  
Muhammad Waseem ◽  
Qian Zhang ◽  
Wang Ke ◽  
Jianhua Zhang ◽  
...  
Keyword(s):  
Lupinus Albus ◽  
Functional Characterization ◽  
Purifying Selection ◽  
White Lupin ◽  
Segmental Duplications ◽  
Chromosomal Distribution ◽  
Systematic Analysis ◽  
Gene Structures ◽  
Adaptive Ability

Abstract Background White lupin (Lupinus albus) is a leguminous crop with elite adaptive ability in phosphorus-deficient soil and used as a model plant for studying phosphorus (P) use. However, the genetic basis of its adaptation to low P (LP) remains unclear. ATPase binding cassette (ABC) transports G subfamily play a crucial role in the transportation of biological molecules across the membrane. To date, identification of this subfamily has been analyzed in some plants, but no systematic analysis of these transporters in phosphorus acquisition is available for white lupin. Results This study identified 66 ABCG gene family members in the white lupin genome using comprehensive approaches. Phylogenetic analysis of white lupin ABCG transporters revealed six subclades based on their counterparts in Arabidopsis, displaying distinct gene structure and motif distribution in each cluster. Influences of the whole genome duplication on the evolution of L.albABCGs were investigated in detail. Segmental duplications appear to be the major driving force for the expansion of ABCGs in white lupin. Analysis of the Ka/Ks ratios indicated that the paralogs of the L.albABCG subfamily members principally underwent purifying selection. However, it was found that L.albABCG29 was a result of both tandem and segmental duplications. Overexpression of L.albABCG29 in white lupin hairy root enhanced P accumulation in cluster root under LP and improved plant growth. Histochemical GUS staining indicated that L.albABCG29 expression increased under LP in white lupin roots. Further, overexpression of L.albABCG29 in rice significantly improved P use under combined soil drying and LP by improving root growth associated with increased rhizosheath formation. Conclusion Through systematic and comprehensive genome-wide bioinformatics analysis, including conserved domain, gene structures, chromosomal distribution, phylogenetic relationships, and gene duplication analysis, the L.albABCG subfamily was identified in white lupin, and L.albABCG29 characterized in detail. In summary, our results provide deep insight into the characterization of the L.albABCG subfamily and the role of L.albABCG29 in improving P use.

scholarly journals Systematic Analysis of the bZIP Family in Tobacco and Functional Characterization of NtbZIP62 Involvement in Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 148
Author(s):  
Zhiyuan Li ◽  
Jiangtao Chao ◽  
Xiaoxu Li ◽  
Gongbo Li ◽  
Dean Song ◽  
...  
Keyword(s):  
Salt Stress ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Segmental Duplications ◽  
Basic Leucine Zipper ◽  
Systematic Analysis ◽  
Duplication Events ◽  
Tobacco Genome ◽  
Gene Structures

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in the tobacco genome were classified into 11 groups with Arabidopsis and tomato bZIP members, based on the results of a phylogenetic analysis. An examination of gene structures and conserved motifs revealed relatively conserved exon/intron structures and motif organization within each group. The results of an investigation of whole-genome duplication events indicated that segmental duplications were crucial for the expansion of the bZIP gene family in tobacco. Expression profiles confirmed that the NtbZIP genes are differentially expressed in various tissues, and several genes are responsive to diverse stresses. Notably, NtbZIP62, which was identified as an AtbZIP37/ABF3 homolog, was highly expressed in response to salinity. Subcellular localization analyses proved that NtbZIP62 is a nuclear protein. Furthermore, the overexpression of NtbZIP62 in tobacco significantly enhanced the salt stress tolerance of the transgenic plants. The results of this study may be relevant for future functional analyses of the bZIP genes in tobacco.

scholarly journals Evolution and Expression of the Membrane Attack Complex and Perforin Gene Family in the Poaceae

2020 ◽  
Vol 21 (16) ◽  
pp. 5736
Author(s):  
Lujun Yu ◽  
Di Liu ◽  
Shiyi Chen ◽  
Yangshuo Dai ◽  
Wuxiu Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Functional Characterization ◽  
Membrane Attack Complex ◽  
Purifying Selection ◽  
Plant Responses ◽  
Segmental Duplications ◽  
Group I ◽  
Poaceae Family ◽  
Duplication Events ◽  
Gene Structures

Membrane Attack Complex and Perforin (MACPF) proteins play crucial roles in plant development and plant responses to environmental stresses. To date, only four MACPF genes have been identified in Arabidopsis thaliana, and the functions of the MACPF gene family members in other plants, especially in important crop plants, such as the Poaceae family, remain largely unknown. In this study, we identified and analyzed 42 MACPF genes from six completely sequenced and well annotated species representing the major Poaceae clades. A phylogenetic analysis of MACPF genes resolved four groups, characterized by shared motif organizations and gene structures within each group. MACPF genes were unevenly distributed along the Poaceae chromosomes. Moreover, segmental duplications and dispersed duplication events may have played significant roles during MACPF gene family expansion and functional diversification in the Poaceae. In addition, phylogenomic synteny analysis revealed a high degree of conservation among the Poaceae MACPF genes. In particular, Group I, II, and III MACPF genes were exposed to strong purifying selection with different evolutionary rates. Temporal and spatial expression analyses suggested that Group III MACPF genes were highly expressed relative to the other groups. In addition, most MACPF genes were highly expressed in vegetative tissues and up-regulated by several biotic and abiotic stresses. Taken together, these findings provide valuable information for further functional characterization and phenotypic validation of the Poaceae MACPF gene family.

scholarly journals Identification of an isoflavonoid transporter required for the nodule establishment of the Rhizobium-Fabaceae symbiotic interaction

2021 ◽  
Author(s):  
Wanda Biala-Leonhard ◽  
Laura Zanin ◽  
Stefano Gottardi ◽  
Rita de Brito Francisco ◽  
Silvia Venuti ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Crop Productivity ◽  
Signaling Cascades ◽  
Nutritional Deficiencies ◽  
White Lupin ◽  
Symbiotic Interaction ◽  
Phosphate Availability ◽  
Rhizobial Symbiosis

Nitrogen (N) as well as Phosphorus (P) are key nutrients determining crop productivity. Legumes have developed strategies to overcome nutrient limitation by e.g., forming a symbiotic relationship with N-fixing rhizobia and the release of P-mobilizing exudates and are thus able to grow without supply of N or P fertilizers. The legume-rhizobial symbiosis starts with root release of isoflavonoids, that act as signaling molecules perceived by compatible bacteria. Subsequently, bacteria release nod factors, which induce signaling cascades allowing the formation of functional N-fixing nodules. We report here the identification and functional characterization of a plasma membrane-localized MATE-type transporter (LaMATE2) involved in the release of genistein from white lupin roots. The LaMATE2 expression in the root is upregulated under N deficiency as well as low phosphate availability, two nutritional deficiencies that induce the release of this isoflavonoid. LaMATE2 silencing reduced genistein efflux and even more the formation of symbiotic nodules, supporting the crucial role of LaMATE2 in isoflavonoid release and nodulation. Furthermore, silencing of LaMATE2 limited the P-solubilization activity of lupin root exudates. Transport assays in yeast vesicles demonstrated that LaMATE2 acts as a proton-driven isoflavonoid transporter.

scholarly journals Functional characterization of a defense-related class-III chitinase promoter from Lupinus albus, active in legume and monocot tissues

2016 ◽  
Vol 146 (4) ◽  
pp. 923-936
Author(s):  
Dean Oelofse ◽  
Inge Gazendam ◽  
Adri Veale ◽  
Arnaud Djami-Tchatchou ◽  
Dave Berger ◽  
...  
Keyword(s):  
Lupinus Albus ◽  
Functional Characterization ◽  
Class Iii ◽  
Class Iii Chitinase

scholarly journals Functional characterization of motif sequences under purifying selection

2013 ◽  
Vol 41 (4) ◽  
pp. 2105-2120 ◽  
Author(s):  
D.-H. Chen ◽  
A. Y.-F. Chang ◽  
B.-Y. Liao ◽  
C.-H. Yeang
Keyword(s):  
Functional Characterization ◽  
Purifying Selection

Identification of genes induced in proteoid roots of white lupin under nitrogen and phosphorus deprivation, with functional characterization of a formamidase

2010 ◽  
Vol 334 (1-2) ◽  
pp. 137-150 ◽  
Author(s):  
Mousumi Rath ◽  
Jay Salas ◽  
Bandita Parhy ◽  
Robert Norton ◽  
Himabindu Menakuru ◽  
...  
Keyword(s):  
Functional Characterization ◽  
White Lupin ◽  
Nitrogen And Phosphorus ◽  
Proteoid Roots ◽  
Phosphorus Deprivation

scholarly journals Key wheat GRF genes constraining wheat tillering of mutant dmc

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11235
Author(s):  
Jing Zhang ◽  
Junchang Li ◽  
Yongjing Ni ◽  
Yumei Jiang ◽  
Zhixin Jiao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Acetic Acid ◽  
Indole Acetic Acid ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Tissue Expression ◽  
Wild Type ◽  
Gene Structures ◽  
Wheat Mutant

Tillering is a key agronomy trait for wheat (Triticum aestivum L.) production. Previously, we have reported a dwarf-monoculm wheat mutant (dmc) obtained from cultivar Guomai 301 (wild type, WT), and found growth regulating factors (GRFs) playing important roles in regulating wheat tillering. This study is to systematically investigate the roles of all the wheat GRFs (T. aestivum GRFs, TaGRFs) in regulating tillering, and screen out the key regulators. A total of 30 TaGRFs were identified and their physicochemical properties, gene structures, conserved domains, phylogenetic relationships and tissue expression profiles were analyzed. The expression levels of all the TaGRFs were significantly lower in dmc than those in WT at early tillering stage, and the abnormal expressions of TaGRF2-7(A, B, D), TaGRF5-7D, TaGRF10-6(A, B, D) and TaGRF11-2A were major causes constraining the tillering of dmc. The transcriptions of TaGRFs were significantly affected by exogenous indole acetic acid (IAA) and gibberellin acid (GA3) applications, which suggested that TaGRFs as well as IAA, GA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of GRF genes in wheat.

scholarly journals Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 275 ◽  
Author(s):  
Cao ◽  
Cheng ◽  
Zhang ◽  
Aslam ◽  
Yan ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Gene Families ◽  
Cellulose Synthase ◽  
Ananas Comosus ◽  
Tropical Fruit ◽  
Genome Wide ◽  
Gene Structures

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple.

scholarly journals Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

2022 ◽  
Vol 12 ◽  
Author(s):  
Bobin Liu ◽  
Juanli Zhu ◽  
Lina Lin ◽  
Qixin Yang ◽  
Bangping Hu ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Southern China ◽  
Gene Families ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Chromosomal Distribution ◽  
Element Analysis ◽  
Genome Wide ◽  
Gene Structures

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

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