Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses

Huang, Xiaolong; Yan, Huiqing; Liu, Yanjing; Yi, Yin

doi:10.1007/s13258-020-00931-x

Cited by 16 publications

(9 citation statements)

References 40 publications

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“…The recent release of moso bamboo draft genome and chromosome level reference genome is the great potential for enabling genetic manipulation of the bamboo gene family [ 22 , 23 ]. Based on the rapid development of genome sequencing technology, the identification of LBD TF genes has been reported in plants such as Oryza sativa [ 13 ], Brassica napus [ 24 ], Gossypium raimondii [ 25 ], Vitis vinifera [ 26 ], Solanum tuberosum [ 11 ], maize [ 27 ], and Physcomitrella patens [ 28 ]. The specific molecular functions of the LBDs have been validated in the model plants Arabidopsis and rice.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

Huang

et al. 2021

BMC Plant Biol

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Background Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). Results In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response–associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT–PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. Conclusions In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

Huang

et al. 2021

BMC Plant Biol

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“…In addition, the expression of this gene was affected by the signal transmission pathway of jasmonic acid. Huang et al (2020) found that most Physcomitrium patens mosses increased the expression of the PpLBDs gene after they were processed by mannitol. They extrapolated that the expression of PpLBDs might strengthen the drought resistance of the mosses.…”

Section: Discussionmentioning

confidence: 99%

“…They are divided into class I and class II following the differences in the LOB domain. LBD transcription factors from the class I contain the complete LOB domain, and they are mainly responsible for plant growth, such as developing lateral organs, extending leaves, and regeneration ( Bell et al., 2012 ; Liu et al., 2018 ; Zhang et al., 2020 ; Huang et al., 2020 ). Class II LBD proteins hold an incomplete leucine zipper-like domain, so they cannot form the coiled-coil structure.…”

Section: Discussionmentioning

confidence: 99%

ZmLBD2 a maize (Zea mays L.) lateral organ boundaries domain (LBD) transcription factor enhances drought tolerance in transgenic Arabidopsis thaliana

et al. 2022

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Maize (Zea mays L.) is an annual gramineous herb and is among the world’s most important crop species. Drought is the main factor contributing to maize yield reduction. The lateral organ boundaries domain (LBD) proteins belong to a class of higher-plant-specific transcription factors. LBD proteins usually include the highly conserved lateral organ boundaries (LOB) domains that play essential roles in plant growth and response to biotic stresses. However, few studies have addressed the biological functions of LBD genes associated with maize response to drought. Here we cloned the ZmLBD2 gene from maize and described its role in combating drought. Investigating ZmLBD2 subcellular localization, we show that it localizes to the cell nucleus and can specifically bind with inverted repeats of “GCGGCG”. Under drought stress, Arabidopsis thaliana overexpressing ZmLBD2 performed better than the wild-type plants in terms of seed germination rates, root length, relative water content, fresh weight, chlorophyll content, proline content, and antioxidant enzyme content. Arabidopsis overexpressing ZmLBD2 contained less MDA, H2O2, and O2− than the wild-type plants. Our protein-protein interaction results indicate an interaction between the ZmLBD2 and ZmIAA5 genes. In conclusion, the ZmLBD2 gene positively regulates H2O2 homeostasis in plants, strengthening drought resistance.

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“…In Arabidopsis, CUC genes are direct upstream regulators of ALOG genes (Takeda et al 2011 ). Both CUC genes and LOB family genes are conserved in mosses, thus, it is expected that further studies on the function of boundary genes will provide novel insights into the evolution of boundary factors and mechanisms of stem cell regulation (Huang et al 2020 ; Xu et al 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes

Hata

Kyozuka

2021

Plant Mol Biol

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Key message This review compares the molecular mechanisms of stem cell control in the shoot apical meristems of mosses and angiosperms and reveals the conserved features and evolution of plant stem cells. Abstract The establishment and maintenance of pluripotent stem cells in the shoot apical meristem (SAM) are key developmental processes in land plants including the most basal, bryophytes. Bryophytes, such as Physcomitrium (Physcomitrella) patens and Marchantia polymorpha, are emerging as attractive model species to study the conserved features and evolutionary processes in the mechanisms controlling stem cells. Recent studies using these model bryophyte species have started to uncover the similarities and differences in stem cell regulation between bryophytes and angiosperms. In this review, we summarize findings on stem cell function and its regulation focusing on different aspects including hormonal, genetic, and epigenetic control. Stem cell regulation through auxin, cytokinin, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling and chromatin modification by Polycomb Repressive Complex 2 (PRC2) and PRC1 is well conserved. Several transcription factors crucial for SAM regulation in angiosperms are not involved in the regulation of the SAM in mosses, but similarities also exist. These findings provide insights into the evolutionary trajectory of the SAM and the fundamental mechanisms involved in stem cell regulation that are conserved across land plants.

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Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses

Cited by 16 publications

References 40 publications

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

Genome-wide identification and expression analysis of LBD transcription factor genes in Moso bamboo (Phyllostachys edulis)

ZmLBD2 a maize (Zea mays L.) lateral organ boundaries domain (LBD) transcription factor enhances drought tolerance in transgenic Arabidopsis thaliana

Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes

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