RNA-Seq Analysis of the Arabidopsis Transcriptome in Pluripotent Calli

Pil Joon Seo,Kyounghee Lee,Ok-Sun Park 한국분자세포생물학회 2016 Molecules and cells Vol.39 No.6

Plant cells have a remarkable ability to induce pluripotent cell masses and regenerate whole plant organs under the appropriate culture conditions. Although the in vitro regeneration system is widely applied to manipulate agronomic traits, an understanding of the molecular mechanisms underlying callus formation is starting to emerge. Here, we performed genome-wide transcriptome profiling of wild-type leaves and leaf explant-derived calli for comparison and identified 10,405 differentially expressed genes (> two-fold change). In addition to the well-defined signaling pathways involved in callus formation, we uncovered additional biological processes that may contribute to robust cellular dedifferentiation. Particular emphasis is placed on molecular components involved in leaf development, circadian clock, stress and hormone signaling, carbohydrate metabolism, and chromatin organization. Genetic and pharmacological analyses further supported that homeostasis of clock activity and stress signaling is crucial for proper callus induction. In addition, gibberellic acid (GA) and brassinosteroid (BR) signaling also participates in intricate cellular reprogramming. Collectively, our findings indicate that multiple signaling pathways are intertwined to allow reversible transition of cellular differentiation and dedifferentiation.

Cold activation of a plasma membrane-tethered NAC transcription factor induces a pathogen resistance response in Arabidopsis

Seo, Pil Joon,Kim, Mi Jung,Park, Ju-Young,Kim, Sun-Young,Jeon, Jin,Lee, Yong-Hwan,Kim, Jungmook,Park, Chung-Mo Blackwell Publishing Ltd 2010 The Plant journal Vol.61 No.4

<P>Summary</P><P>Cold signals interact with other environmental cues to modulate plant developmental processes. Recent studies have shown that many <I>Pathogenesis-Related</I> (<I>PR</I>) genes are induced and disease resistance is enhanced after exposure to low temperatures, linking cold signals with pathogenesis in plants. However, the underlying molecular mechanisms and signaling schemes are largely unknown. Here, we demonstrate that cold stimulates proteolytic activation of a plasma membrane-tethered NAC (NAM/ATAF1/2/CUC2) transcription factor NTL6. The transcriptionally active NTL6 protein enters the nucleus, where it induces a subset of <I>PR</I> genes by directly binding to a conserved sequence in the promoters of cold-responsive <I>PR</I> genes, such as <I>PR1</I>, <I>PR2</I>, and <I>PR5</I>. While transgenic plants overexpressing an active NTL6 form exhibited enhanced disease resistance, RNAi plants with reduced NTL6 activity were more susceptible to pathogen infection at low temperatures. Accordingly, cold induction of <I>PR1</I> disappeared in the RNAi plants. Consistent with the close relationship between cold and pathogenesis, cold-acclimated plants showed enhanced resistance to pathogen infection. In this signaling cascade, controlled activation of the membrane-tethered, dormant NTL6 transcription factor serves as a molecular link that incorporates cold signals into pathogen resistance responses. However, the NTL6-mediated cold induction of the <I>PR</I> genes is independent of salicylic acid (SA). The <I>PR</I> genes were still induced by SA in the <I>NTL6</I> RNAi plants. Cold regulation of the <I>PR</I> genes through the membrane-mediated transcriptional control is thought to be an adaptive process that ensures quick plant responses to incoming pathogens that frequently occur during cold seasons.</P>

Targeted inactivation of transcription factors by overexpression of their truncated forms in plants

Seo, Pil Joon,Hong, Shin‐,Young,Ryu, Jae Yong,Jeong, Eun‐,Young,Kim, Sang‐,Gyu,Baldwin, Ian T.,Park, Chung‐,Mo Blackwell Publishing Ltd 2012 The Plant journal Vol.72 No.1

<P><B>Summary</B></P><P>Transcription factors are central constituents of gene regulatory networks that control diverse aspects of plant development and environmental adaptability. Therefore they have been explored for decades as primary targets for agricultural biotechnology. A gene of interest can readily be introduced into many crop plants, whereas targeted gene inactivation is practically difficult in many cases. Here, we developed an artificial small interfering peptide (a‐siPEP) approach, which is based on overexpression of specific protein domains, and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, <I>Brachypodium</I>. We designed potential a‐siPEPs of two representative MADS box transcription factors, SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG), and a MYB transcription factor, LATE ELONGATED HYPOCOTYL (LHY). Transgenic plants overproducing the a‐siPEPs displayed phenotypes comparable to those of gene‐deficient mutants. The a‐siPEPs attenuate nuclear import and DNA‐binding of target transcription factors. Our data demonstrate that the a‐siPEP tool is an efficient genetic means of inactivating specific transcription factors in plants.</P>

Peptide interference (PEPi) as a protein knockout system for transcription factors in plants

Pil Joon Seo,Sangmin Lee,Chung-Mo Park 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Targeted gene silencing is an essential component of plant biotechnology. RNA interference is often employed for targeted gene silencing in plants. However, it suffers from off-target effects and unstable gene suppression in many cases. In recent years, engineered nuclease-based tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have been developed to induce site-specific genome modifications. However, these approaches require much time and labor for extensive screening of mutants. We have recently reported that the activities of dimeric transcription factors are competently suppressed by genome-encoded small interfering peptides (siPEPs) that competitively form nonfunctional heterodimers in plants. In addition, some splice variants of transcription factors also act in a similar manner to negatively regulate the activities of specific transcription factors. We designated the siPEP-mediated suppression of transcription factors peptide interference (PEPi). Based on our previous observations, we also developed an artificial siPEP (a-siPEP) approach and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, Brachypodium. We designed a series of potential a-siPEPs of two representative transcription factors SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG) that function in flowering induction and floral organogenesis, respectively. Transgenic plants overproducing a-siPEPs displayed phenotypes comparable to those of gene-deficient mutants. Collectively, our data demonstrate that the siPEP tool is an efficient protein knockout system for inactivating specific transcription factors, and other multimeric enzymes and membrane transporters as well, in plants. We will discuss about the global application of the siPEP toll to other plant species and potential advantages over other gene manipulation tools.

Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions

Seo, Pil Joon,Park, Mi-Jeong,Park, Chung-Mo Springer-Verlag 2013 Planta Vol.237 No.6

<P>Transcription factors play a central role in the gene regulatory networks that mediate various aspects of plant developmental processes and responses to environmental changes. Therefore, their activities are elaborately regulated at multiple steps. In particular, accumulating evidence illustrates that post-transcriptional control of mRNA metabolism is a key molecular scheme that modulates the transcription factor activities in plant responses to temperature fluctuations. Transcription factors have a modular structure consisting of distinct protein domains essential for DNA binding, dimerization, and transcriptional regulation. Alternative splicing produces multiple proteins having different structural domain compositions from a single transcription factor gene. Recent studies have shown that alternative splicing of some transcription factor genes generates small interfering peptides (siPEPs) that negatively regulate the target transcription factors via peptide interference (PEPi), constituting self-regulatory circuits in plant cold stress response. A number of splicing factors, which are involved in RNA binding, splice site selection, and spliceosome assembly, are also affected by temperature fluctuations, supporting the close association of alternative splicing of transcription factors with plant responses to low temperatures. In this review, we summarize recent progress on the temperature-responsive alternative splicing of transcription factors in plants with emphasis on the siPEP-mediated PEPi mechanism.</P>

Controlled turnover of CONSTANS protein by the HOS1 E3 ligase regulates floral transition at low temperatures.

Joon Seo, Pil,Jung, Jae-Hoon,Park, Mi-Jeong,Lee, Kyounghee,Park, Chung-Mo Landes Bioscience 2013 Plant signaling & behavior Vol.8 No.4

<P>The timing of flowering is coordinately regulated by complex gene regulatory networks that integrate developmental and environmental cues. Light and temperature are major environmental determinants in flowering time control. Temperature signals include two major categories: ambient temperature signals and cold nonfreezing temperature signals. Notably, the effects of cold temperatures on flowering timing are profoundly differentiated, depending on the duration of cold exposure. Whereas long-term exposure to cold temperatures, designated vernalization, promotes flowering, short-term cold exposure delays flowering. Genes constituting the vernalization pathway and underlying molecular mechanisms have been extensively studied. However, how cold stress signals delay flowering is largely unknown. We have recently reported that the HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1)-CONSTANS (CO) module is at least partly responsible for the daily sensing of cold stress signals in flowering time control. Intermittent cold stress triggers the degradation of CO, a central activator of photoperiodic flowering, via a ubiquitination pathway that involves the HOS1 E3 ubiquitin ligase, leading to suppression of FLOWERING LOCUS T (FT) gene and delayed flowering. It is proposed that CO serves as a molecular knot that integrates photoperiod and temperature signals into the flowering pathways, fine-tuning photoperiodic flowering under short-term temperature fluctuations.</P>

Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in <i>Arabidopsis</i>

Seo, Pil Joon,Ryu, Jaeyong,Kang, Seok Ki,Park, Chung‐,Mo Blackwell Publishing Ltd 2011 The Plant journal Vol.65 No.3

<P><B>Summary</B></P><P>There has been a long‐standing interest in the role played by sugars in flowering. Of particular interest is how sugar‐related signals are integrated into flowering genetic pathways. Here, we demonstrate that the INDETERMINATE DOMAIN transcription factor AtIDD8 regulates photoperiodic flowering by modulating sugar transport and metabolism. We found that whereas <I>AtIDD8</I>‐deficient <I>idd8</I> mutants exhibit delayed flowering under long days, <I>AtIDD8</I>‐overexpressing plants (35S:<I>IDD8</I>) show early flowering. In addition, the sucrose synthase genes <I>SUS1</I> and <I>SUS4</I> were upregulated in 35S:<I>IDD8</I> plants but downregulated in <I>idd8</I> mutants, in which endogenous sugar levels were altered. AtIDD8 activates the <I>SUS4</I> gene by binding directly to its promoter, resulting in promoted flowering in <I>SUS4‐</I>overexpressing plants. <I>SUS4</I> expression also responds to photoperiodic signals. Notably, the <I>AtIDD8</I> gene is suppressed by sugar deprivation. Therefore, we conclude that AtIDD8 regulation of sugar transport and metabolism is linked to photoperiodic flowering.</P>

An Arabidopsis senescence-associated protein SAG29 regulates cell viability under high salinity

Seo, Pil Joon,Park, Jung-Min,Kang, Seok Ki,Kim, Sang-Gyu,Park, Chung-Mo Springer-Verlag 2011 Planta Vol.233 No.1

Multiple Layers of Posttranslational Regulation Refine Circadian Clock Activity in <i>Arabidopsis</i>

Seo, Pil Joon,Mas, Paloma American Society of Plant Biologists 2014 The Plant cell Vol.26 No.1

<P>The circadian clock is a cellular time-keeper mechanism that regulates biological rhythms with a period of ∼24 h. The circadian rhythms in metabolism, physiology, and development are synchronized by environmental cues such as light and temperature. In plants, proper matching of the internal circadian time with the external environment confers fitness advantages on plant survival and propagation. Accordingly, plants have evolved elaborated regulatory mechanisms that precisely control the circadian oscillations. Transcriptional feedback regulation of several clock components has been well characterized over the past years. However, the importance of additional regulatory mechanisms such as chromatin remodeling, protein complexes, protein phosphorylation, and stability is only starting to emerge. The multiple layers of circadian regulation enable plants to properly synchronize with the environmental cycles and to fine-tune the circadian oscillations. This review focuses on the diverse posttranslational events that regulate circadian clock function. We discuss the mechanistic insights explaining how plants articulate a high degree of complexity in their regulatory networks to maintain circadian homeostasis and to generate highly precise waveforms of circadian expression and activity.</P>

The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis.

Seo, Pil Joon,Xiang, Fengning,Qiao, Meng,Park, Ju-Young,Lee, Young Na,Kim, Sang-Gyu,Lee, Yong-Hwan,Park, Woong June,Park, Chung-Mo American Society of Plant Physiologists 2009 Plant Physiology Vol.151 No.1

<P>Plant adaptive responses to drought are coordinated by adjusting growth and developmental processes as well as molecular and cellular activities. The root system is the primary site that perceives drought stress signals, and its development is profoundly affected by soil water content. Various growth hormones, particularly abscisic acid (ABA) and auxin, play a critical role in root growth under drought through complex signaling networks. Here, we report that a R2R3-type MYB transcription factor, MYB96, regulates drought stress response by integrating ABA and auxin signals. The MYB96-mediated ABA signals are integrated into an auxin signaling pathway that involves a subset of GH3 genes encoding auxin-conjugating enzymes. A MYB96-overexpressing Arabidopsis (Arabidopsis thaliana) mutant exhibited enhanced drought resistance with reduced lateral roots. In the mutant, while lateral root primordia were normally developed, meristem activation and lateral root elongation were suppressed. In contrast, a T-DNA insertional knockout mutant was more susceptible to drought. Auxin also induces MYB96 primarily in the roots, which in turn induces the GH3 genes and modulates endogenous auxin levels during lateral root development. We propose that MYB96 is a molecular link that mediates ABA-auxin cross talk in drought stress response and lateral root growth, providing an adaptive strategy under drought stress conditions.</P>