Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

Shen, Yue; Liu, Mingzhe; Wang, Lili; Li, Zhuowei; Taylor, David C.; Li, Zhixi; Zhang, Meng

doi:10.1007/s00438-015-1156-x

Cited by 18 publications

(27 citation statements)

References 69 publications

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“…Motif 4 is a 30–50 residue domain present close to the N-terminus and is found in many CLO/PXG sequences throughout the Viridiplantae (and Fungi). This Motif is characteristic of the so-called H-caleosins (where H = high molecular weight), as previously reported from several labs [ 1 , 2 , 27 , 28 , 64 – 66 ]. We found that all Angiosperm genomes sequenced to date contain at least one copy each of the L- and H-caleosin sequences and although the evidence is less clear for the other Viridiplantae, it seems that most species also contain both isoforms.…”

Section: Resultssupporting

confidence: 80%

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae

et al. 2018

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Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10–12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30–50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.

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Section: Resultssupporting

confidence: 80%

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae

et al. 2018

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“…Our finding was consistent with previous evolutionary analyses. In addition, by comparing the gene family “intron–exon” number, length, distribution and other genetic structure, we can understand the genetic structure of the diversity and complexity of the reasons for the formation ( Shen et al., 2016 ). We found that in the OPT clade, 11 of 15 BrrOPTs contained 4–6 exons, similar to Arabidopsis , rice, Populus , and Vitis (4–7) ( Cao et al., 2011 ).…”

Section: Resultsmentioning

confidence: 99%

“…Gene duplication events are thought to have frequently occurred in organismal evolution ( Kent et al., 2003 , Mehan et al., 2004 ). Genome-wide duplication events, gene loss, and local rearrangements have created the present complexities of the genome ( Shen et al., 2016 ). In addition, we found that the turnip underwent broad-scale gene duplication events, OPT genes located chromosome duplicate region ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

Yang

Yin

et al. 2018

Plant Diversity

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Oligopeptide transporters (OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities. Here, 28 BrrOPT genes were identified in the turnip. Phylogenetic analyses revealed two well-supported clades in the OPT family, containing 15 BrrOPTs and 13 BrrYSLs. The exon/intron structure of OPT clade are conserved but the yellow stripe-like (YSL) clade was different. The exon/intron of the YSL clade possesses structural differences, whereas the YSL class motifs structure are conserved. The OPT genes are distributed unevenly among the chromosomes of the turnip genome. Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication. For the expression profiles at different developmental stages, a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family. Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution. Furthermore, BrrOPT8.1, BrrYSL1.2, BrrYSL1.3, BrrYSL6 and BrrYSL9 responded to Fe(II) treatments and BrrYSL7 responded to calcium treatments, BrrYSL6 responded to multiple treatments in root, suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies. Our data provide important information for further functional dissection of BrrOPTs, especially in transporting metal ions and nutrient deficiency stress adaptation.

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“…The lipid‐associated Ca 2+ binding ability also occurs in fungi and green algae (Naested et al ., 2000; Hanano et al ., 2006; Rahman et al ., 2018). Caleosin gene families have been annotated in castor bean and flax (Hyun et al ., 2013); wheat, barley, rye, rice and Brachypodium (Khalil et al ., 2014); Arabidopsis (Shen et al ., 2014); Brassicaceae (Shen et al ., 2016) and hazelnut (Lamberti et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

OsClo5 functions as a transcriptional co‐repressor by interacting with OsDi19‐5 to negatively affect salt stress tolerance in rice seedlings

Pei

Kong

et al. 2020

The Plant Journal

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Significance Statement Caleosins constitute a small protein family with one calcium‐binding EF‐hand motif. They are involved in the responses to development and abiotic stresses in plants. Nevertheless, how they impact salt stress tolerance in rice is largely unknown. In this study, OsClo5 has been demonstrated to function as a transcriptional co‐repressor by interacting with OsDi19‐5 to negatively affect salt stress tolerance in rice seedlings, and a working model was established to explain this phenomena.

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Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

Cited by 18 publications

References 69 publications

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae

Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family

OsClo5 functions as a transcriptional co‐repressor by interacting with OsDi19‐5 to negatively affect salt stress tolerance in rice seedlings

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