Genome-wide analysis of the IQD gene family in maize

Cai, Ronghao; Zhang, Congsheng; Zhao, Yang; Zhu, Kejun; Wang, Yufu; Jiang, Haiyang; Xiang, Yan; Cheng, Beijiu

doi:10.1007/s00438-015-1122-7

Cited by 35 publications

(36 citation statements)

References 52 publications

(64 reference statements)

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“…Previous studies have reported that IQD1 and IQD20 can interact with CaM in Arabidopsis 6 7 . Recently, it was proposed that ZmIQD15 can interact with CaM in vitro 18 . To attest whether this interaction also occurs in moso bamboo, yeast two-hybrid analysis was adopted to examine the interaction between PeIQDs and PeCaM2 .…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Chen

et al. 2016

Sci Rep

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Members of the plant-specific IQ67-domain (IQD) protein family are involved in various aspects of normal plant growth and developmental processes as well as basal defence response. Although hundreds of IQD proteins have been identified, only a small number of IQDs have been functionally characterized. Moreover, no systematic study has been performed on moso bamboo. In this study, we performed for the first time a genome-wide identification and expression analysis of the IQD gene family in moso bamboo. We identified 29 non-redundant PeIQD encoding genes. Analysis of the evolutionary patterns and divergence revealed that the IQD genes underwent a large-scale event around 12 million years ago and the division times of IQD family genes between moso bamboo and rice, and, between moso bamboo and Brachypodium, were found to be 20–35 MYA and 25–40 MYA, respectively. We surveyed the putative promoter regions of the PeIQD genes, which showed that largely stress-related cis-elements existed in these genes. The expression profiles of the IQD genes shed light on their functional divergence. Additionally, a yeast two-hybrid assay proved that PeIQD8 can interact with PeCaM2 and that IQ or I in the IQ motif is required for PeIQD8 to combine with CaM2.

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Section: Resultsmentioning

confidence: 99%

“…The IQD genes are also regulated by drought treatment. For example, the PtIQDIII members and ZmIQD genes have been testified 12 18 . Base on the phylogenetic analysis of IQD members, we used further qRT-PCR to investigate the expression patterns of PeIQD family genes under MeJA and drought treatments.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Chen

et al. 2016

Sci Rep

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“…Based on the occurrence of one IQD-like gene in P. patens and nine in Pinus sp., IQD gene family is believed to originated prior to bryophyte and/ or vascular plants divergence (i.e., 450-700 MYA), but before the divergence of gymnosperms and angiosperms 300 MYA [33,34]. The comprehensive genome-wide analysis of IQDs has been extensively carried out in many model and non-model plants, such as Arabidopsis, rice [33], maize [35], soybean [36], poplar [37], and tomato [38]. A precise and systemic characterization of IQD gene family in grapevine…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera)

Liu

Haider

Khan

et al. 2020

Genes

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The plant-specific IQ67-domain (IQD) protein family members are downstream targets of calcium sensors, known to regulate plant growth and lateral organ polarity, and basal defense response against environmental cues. No systematic study of IQD gene family has been performed on grapevine. The public availability of grapevine genome enables us to perform identification, phylogeny, chromosomal orientation, and gene structure analysis of the IQD genes in grapevine. We identified 49 VvIQD genes (VvIQD1–VvIQD49) and further classified them into eight subgroups based on phylogenetic relationships. The 49 VvIQD genes were assigned to 19 different chromosomal positions. The collinear relationship between grapevine and Arabidopsis IQDs (VvIQD and AtIQD), and within grapevine VvIQDs, was highly conserved. In addition, most of duplicated gene pairs showed Ka/Ks ratio less than 1.00, indicating purifying selection within these gene pairs, implying functional discrepancy after duplication. Transcription profiling of VvIQD genes shed light on their specific role in grapevine tissue and organ development. The qRT-PCR validation of the 49 VvIQD genes in grape berry tissue from cultivars with distinct berry shape during developmental phases suggested candidate genes involved in the shape of grape berries. The subcellular prediction of VvIQD22, VvIQD23, VvIQD38, and VvIQD49 genes validated their localization in the nucleus and plasma membrane. The VvIQD49 protein interaction with VvCaM2 was also verified by bimolecular fluorescence complementation (BiFC) analysis in the plasma membrane. Our findings will be valuable for the functional genomic studies for desirable shape development of grape berries.

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“…The founding member of the IQD family, IQD1 from Arabidopsis thaliana , was found in a screen of T-DNA activation tagged lines for novel regulators of glucosinolates, a class of defense-related metabolites, and overexpression of AtIQD1 in transgenic Arabidopsis plants was reported to stimulate glucosinolate accumulation and plant defense. 1 Subsequently, IQD families have been systematically annotated in the genomes of Arabidopsis and rice ( Oryza sativa ), 2 and more recently in several additional angiosperms, including tomato ( Solanum lycopersicum ) 3 and maize ( Zea mays ), 4 where they are encoded by multigene families of 23 to 67 members. The protein family is defined by the central conserved IQ67-domain, which spans 67 amino acids and contains up to three IQ motifs required for binding to CaM Ca 2+ sensors.…”

mentioning

confidence: 99%

“…The protein family is defined by the central conserved IQ67-domain, which spans 67 amino acids and contains up to three IQ motifs required for binding to CaM Ca 2+ sensors. 4,5 On both sites, the IQ67 domain is flanked by large regions of predicted intrinsic disorder, interspersed only by short IQD-specific motifs of unknown functions. 2,6 Phylogenetic analyses of IQD families from angiosperms indicate the presence of four subgroups that mostly differ in the distribution of IQD-specific motifs.…”

mentioning

confidence: 99%

Functions of IQD proteins as hubs in cellular calcium and auxin signaling: A toolbox for shape formation and tissue-specification in plants?

Bürstenbinder

Mitra

Quegwer

2017

Plant Signaling & Behavior

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Calcium (Ca2+) ions play pivotal roles as second messengers in intracellular signal transduction, and coordinate many biological processes. Changes in intracellular Ca2+ levels are perceived by Ca2+ sensors such as calmodulin (CaM) and CaM-like (CML) proteins, which transduce Ca2+ signals into cellular responses by regulation of diverse target proteins. Insights into molecular functions of CaM targets are thus essential to understand the molecular and cellular basis of Ca2+ signaling. During the last decade, IQ67-domain (IQD) proteins emerged as the largest class of CaM targets in plants with mostly unknown functions. In the March issue of Plant Physiology, we presented the first comprehensive characterization of the 33-membered IQD family in Arabidopsis thaliana. We showed, by analysis of the subcellular localization of translational green fluorescent protein (GFP) fusion proteins, that most IQD members label microtubules (MTs), and additionally often localize to the cell nucleus or to membranes, where they recruit CaM Ca2+ sensors. Important functions at MTs are supported by altered MT organization and plant growth in IQD gain-of-function lines. Because IQD proteins share structural hallmarks of scaffold proteins, we propose roles of IQDs in the assembly of macromolecular complexes to orchestrate Ca2+ CaM signaling from membranes to the nucleus. Interestingly, expression of several IQDs is regulated by auxin, which suggests functions of IQDs as hubs in cellular auxin and calcium signaling to regulate plant growth and development.

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Genome-wide analysis of the IQD gene family in maize

Cited by 35 publications

References 52 publications

Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Genome-wide identification and expression analysis of the IQD gene family in moso bamboo (Phyllostachys edulis)

Comprehensive Sequence Analysis of IQD Gene Family and their Expression Profiling in Grapevine (Vitis vinifera)

Functions of IQD proteins as hubs in cellular calcium and auxin signaling: A toolbox for shape formation and tissue-specification in plants?

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