Signaling and gene regulatory programs in plant vascular stem cells

Zhou, Jing; Sebastián, José; Lee, Ji‐Young

doi:10.1002/dvg.20795

Cited by 13 publications

(10 citation statements)

References 188 publications

(198 reference statements)

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“…The most frequent TF families present in the networks are bHLH, bZIP, ERF, C2H2, G2-like, GATA, HD-ZIP, NAC, MYB, MYB-related, TALE, Trihelix, and WRKY. TFs previously reported as important regulatory genes in stem tissue are present in the networks, including known stem TF hubs such as PHB, ATHB15, APL, VND7, KNAT1, MYB42, and MYB52 (McConnell et al , 2001; Ye, 2002; Emery et al , 2003; Kubo et al , 2005; Floyd, Zalewski and Bowman, 2006; Hoon Jung and Mo Park, 2007; Zhong et al , 2008; Zhou, Sebastian and Lee, 2011; De Rybel et al , 2016; Hennet et al , 2020). Radial patterning of the vascular bundles is established by TF hubs from class III HD-ZIPs, PHB, ATHB15 (McConnell et al , 2001; Emery et al , 2003; Floyd, Zalewski and Bowman, 2006).…”

Section: Resultsmentioning

confidence: 99%

“…NACs are reported to be TF hubs that can induce xylem cell differentiation (Kubo et al , 2005; Zhong et al , 2008). For example, VND7 (NAC TF Family) initiates metaxylem vessel differentiation and induces hierarchical gene expression network by inducing other TFs such as MYBs, which in turn function as secondary and tertiary regulators of genes related to secondary cell wall thickening during xylem cell differentiation (Ye, 2002; Hoon Jung and Mo Park, 2007; Zhou, Sebastian and Lee, 2011; De Rybel et al , 2016).…”

Section: Resultsmentioning

confidence: 99%

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Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Arachchilage

Mullet

Marshall‐Colón

2020

Preprint

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The genetic engineering of value-added traits such as the accumulation of bioproducts 21 in high biomass C4 grass stems is one promising strategy to make plant-derived biofuels more 22 economical for industrial use. A first step toward achieving this goal is to identify stem-specific 23 promoters that can drive the expression of genes of interest with good temporal and spatial 24 specificity. However, a comprehensive characterization of the spatial-temporal regulatory 25 elements of stem tissue-specific promoters for C4 grasses has not been reported. Therefore, we 26 performed an in-silico analysis on Sorghum bicolor cv BTx623 transcriptomes from multiple 27 tissues over development to identify stem-expressed genes. The analysis identified 10 genes that 28 are "Always-On-Stem-Specific," 59 genes that are "Temporally-Stem-Specific during early 29 development," and 21 genes that are "Temporally-Stem-Specific during late development." 30 Promoter analysis revealed common and/or unique cis-regulatory elements in promoters of genes within each of the three categories. Subsequent gene regulatory network (GRN) analysis revealed 32 that different transcriptional regulatory programs are responsible for the temporal activation of the 33 stem-expressed genes. The analysis of temporal stem GRNs between sweet (cv Della) and grain 34 (cv BTx623) sorghum varieties revealed genetic variation that could influence the regulatory 35 landscape. This study provides new insights about sorghum stem biology, and information for 36 future genetic engineering efforts to fine-tune the spatial-temporal expression of transgenes in C4 37 grass stems. 38 39 40 High biomass grasses, such as sorghum (Sorghum bicolor), miscanthus (Miscanthus x 41 giganteus), switchgrass (Panicum virgatum), and sugarcane (Saccharum sp.), offer an abundant 42 and renewable source of biomass for biofuels production (McLaughlin and Kszos, 2005; Rooney 43 et al.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Arachchilage

Mullet

Marshall‐Colón

2020

Preprint

View full text Add to dashboard Cite

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“…By contrast, general reduction in polar auxin transport and down-regulation of auxin signaling genes were observed during the phase of cambium dormancy [52,53]. Consistently, disruption in auxin signaling/responsiveness led to detrimental effects on cambial activities, reducing secondary growth in hybrid aspen plants [54,55]. Similarly, several other plant hormones, in particular cytokinin, ethylene and gibberellins are known to regulate cambial development [56,57].…”

Section: Discussionmentioning

confidence: 99%

Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

Cui

Zhang

et al. 2013

BMC Plant Biol

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BackgroundAs one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocycla cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.ResultsOur anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.ConclusionsThis is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.

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“…The HOMEODOMAIN-LEUCINE ZIPPER Class III ( HD-ZIP III ) genes are key regulators of shoot and root meristems (reviewed by [ 16 ], [ 17 ]). In Arabidopsis , the HD-ZIP III family consists of five members: PHABULOSA ( PHB ), PHAVOLUTA ( PHV ), CORONA ( CNA ), REVOLUTA ( REV ), and ARABIDOPSIS THALIANA HOMEOBOX8 ( ATHB8 ) [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

PHABULOSA Controls the Quiescent Center-Independent Root Meristem Activities in Arabidopsis thaliana

et al. 2015

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Plant growth depends on stem cell niches in meristems. In the root apical meristem, the quiescent center (QC) cells form a niche together with the surrounding stem cells. Stem cells produce daughter cells that are displaced into a transit-amplifying (TA) domain of the root meristem. TA cells divide several times to provide cells for growth. SHORTROOT (SHR) and SCARECROW (SCR) are key regulators of the stem cell niche. Cytokinin controls TA cell activities in a dose-dependent manner. Although the regulatory programs in each compartment of the root meristem have been identified, it is still unclear how they coordinate one another. Here, we investigate how PHABULOSA (PHB), under the posttranscriptional control of SHR and SCR, regulates TA cell activities. The root meristem and growth defects in shr or scr mutants were significantly recovered in the shr phb or scr phb double mutant, respectively. This rescue in root growth occurs in the absence of a QC. Conversely, when the modified PHB, which is highly resistant to microRNA, was expressed throughout the stele of the wild-type root meristem, root growth became very similar to that observed in the shr; however, the identity of the QC was unaffected. Interestingly, a moderate increase in PHB resulted in a root meristem phenotype similar to that observed following the application of high levels of cytokinin. Our protoplast assay and transgenic approach using ARR10 suggest that the depletion of TA cells by high PHB in the stele occurs via the repression of B-ARR activities. This regulatory mechanism seems to help to maintain the cytokinin homeostasis in the meristem. Taken together, our study suggests that PHB can dynamically regulate TA cell activities in a QC-independent manner, and that the SHR-PHB pathway enables a robust root growth system by coordinating the stem cell niche and TA domain.

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Signaling and gene regulatory programs in plant vascular stem cells

Cited by 13 publications

References 188 publications

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Sorghum bicolorcultivars have divergent and dynamic gene regulatory networks that control the temporal expression of genes in stem tissue

Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

PHABULOSA Controls the Quiescent Center-Independent Root Meristem Activities in Arabidopsis thaliana

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