Roles of lignin biosynthesis and regulatory genes in plant development

Yoon, Jinmi,Choi, Heebak,An, Gynheung John Wiley and Sons Inc. 2015 Journal of integrative plant biology Vol.57 No.11

<P><B>Abstract</B></P><P>Lignin is an important factor affecting agricultural traits, biofuel production, and the pulping industry. Most lignin biosynthesis genes and their regulatory genes are expressed mainly in the vascular bundles of stems and leaves, preferentially in tissues undergoing lignification. Other genes are poorly expressed during normal stages of development, but are strongly induced by abiotic or biotic stresses. Some are expressed in non‐lignifying tissues such as the shoot apical meristem. Alterations in lignin levels affect plant development. Suppression of lignin biosynthesis genes causes abnormal phenotypes such as collapsed xylem, bending stems, and growth retardation. The loss of expression by genes that function early in the lignin biosynthesis pathway results in more severe developmental phenotypes when compared with plants that have mutations in later genes. Defective lignin deposition is also associated with phenotypes of seed shattering or brittle culm. MYB and NAC transcriptional factors function as switches, and some homeobox proteins negatively control lignin biosynthesis genes. Ectopic deposition caused by overexpression of lignin biosynthesis genes or master switch genes induces curly leaf formation and dwarfism.</P>

Pleiotropic properties of GOLDEN2-LIKE transcription factors for crop improvement

Kim Sangyun,Choi Heebak,Yi Taegyu,Gwak Dohoon,Ha Sun-Hwa 한국응용생명화학회 2023 Applied Biological Chemistry (Appl Biol Chem) Vol.66 No.-

Crop improvement can be affected by enhancing the efficiency of photosynthesis-associated bioprocesses such as chlorophyll biosynthesis, chloroplast biogenesis, the functioning of photosystems including light-harvesting complexes, and carbon fixation. To achieve this, the GOLDEN2-LIKE (GLK) transcription factors represent promising targets since they play a positive role for greening traits in diverse plants. To scrutinize the pleiotropic impact of GLKs, we summarized all phenotypic traits reported in functional studies that used transgenic approaches to lose or gain gene functions. Additionally, we also discussed altered plant phenotypes with respect to their physiological–biochemical aspects and environmental stress responses. From these results, we conclude that GLKs consistently increase chlorophyll biosynthesis, enhance chloroplast division, and increase photosynthetic rate. They individually influence other traits including yield, phytochemical accumulation, and biotic and abiotic stress resistance. Collectively, GLKs have potential as key regulators to effect increases in overall agricultural quality across plant species. This suggests that they may be among the most promising target genes for future agro-biotechnology applications.

Identification of root-preferential transcription factors in rice by analyzing GUS expression patterns of T-DNA tagging lines

Jinhuan Wei,Yunfei Wu,Lae-Hyeon Cho,Jinmi Yoon,Heebak Choi,Hyeryung Yoon,Ping Jin,Jakyung Yi,Yang-Seok Lee,Hee Joong Jeong,Jungil Yang,Gynheung An 한국식물학회 2017 Journal of Plant Biology Vol.60 No.3

T-DNA tagging lines are useful for analyzing the functions of genes and regulatory elements. We have previously generated approximately 100,000 insertional mutants in japonica rice (Oryza sativa), using T-DNA vectors carrying the promoter-less GUS reporter gene. In this study, we conducted GUS assays of seedlings from 430 lines in which TDNA was inserted into transcription factor genes. Among the 75 lines that showed GUS signals, nine displayed an endospermpreferential expression pattern; two lines demonstrated GUS signals in both endosperm and roots; 21 lines had GUS expression mainly in leaves; 19 lines showed GUS signal in both leaves and roots; and 24 lines expressed GUS predominantly in the roots. Co-segregation analyses of 49 homozygous lines indicated that the GUS expression patterns observed from 38 lines were due to the T-DNA insertion. We also identified fusion transcripts between tagged genes and the GUS reporter in six lines. Quantitative RT-PCR confirmed that the GUS expression patterns of those tagged lines indeed represent organ- and tissue-preferential expression of the tagged genes. The GUS-tagged transcription factor lines identified here will be useful for functional analysis of these candidates.

Genome-wide identification and analysis of <i>Japonica</i> and <i>Indica</i> cultivar-preferred transcripts in rice using 983 Affymetrix array data

Jung, Ki-Hong,Gho, Hyun-Jung,Giong, Hoi-Khoanh,Chandran, Anil Kumar Nalini,Nguyen, Quynh-Nga,Choi, HeeBak,Zhang, Tian,Wang, Wen,Kim, Jin-Hyun,Choi, Hong-Kyu,An, Gynheung Springer New York 2013 Rice Vol.6 No.-

<P><B>Background</B></P><P>Accumulation of genome-wide transcriptome data provides new insight on a genomic scale which cannot be gained by analyses of individual data. The majority of rice (<I>O. sativa</I>) species are <I>japonica</I> and <I>indica</I> cultivars. Genome-wide identification of genes differentially expressed between <I>japonica</I> and <I>indica</I> cultivars will be very useful in understanding the domestication and evolution of rice species.</P><P><B>Results</B></P><P>In this study, we analyzed 983 of the 1866 entries in the Affymetrix array data in the public database: 595 generated from <I>indica</I> and 388 from <I>japonica</I> rice cultivars. To discover differentially expressed genes in each cultivar, we performed significance analysis of microarrays for normalized data, and identified 490 genes preferentially expressed in <I>japonica</I> and 104 genes in <I>indica</I>. Gene Ontology analyses revealed that defense response-related genes are significantly enriched in both cultivars, indicating that <I>japonica</I> and <I>indica</I> might be under strong selection pressure for these traits during domestication. In addition, 36 (34.6%) of 104 genes preferentially expressed in <I>indica</I> and 256 (52.2%) of 490 genes preferentially expressed in <I>japonica</I> were annotated as genes of unknown function. Biotic stress overview in the MapMan toolkit revealed key elements of the signaling pathway for defense response in <I>japonica</I> or <I>indica</I> eQTLs.</P><P><B>Conclusions</B></P><P>The percentage of screened genes preferentially expressed in <I>indica</I> was 4-fold higher (34.6%) and that in <I>japonica</I> was 5-fold (52.2%) higher than expected (11.1%), suggesting that genes of unknown function are responsible for the novel traits that distinguish <I>japonica</I> and <I>indica</I> cultivars. The identification of 10 functionally characterized genes expressed preferentially in either <I>japonica</I> or <I>indica</I> highlights the significance of our candidate genes during the domestication of rice species. Functional analysis of the roles of individual components of stress-mediated signaling pathways will shed light on potential molecular mechanisms to improve disease resistance in rice.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-6-19) contains supplementary material, which is available to authorized users.</P>

<i>OsCOL4</i> is a constitutive flowering repressor upstream of <i>Ehd1</i> and downstream of <i>OsphyB</i>

Lee, Yang-Seok,Jeong, Dong-Hoon,Lee, Dong-Yeon,Yi, Jakyung,Ryu, Choong-Hwan,Kim, Song L.,Jeong, Hee J.,Choi, Sang C.,Jin, Ping,Yang, Jungil,Cho, Lae-Hyeon,Choi, Heebak,An, Gynheung Blackwell Publishing Ltd 2010 The Plant journal Vol.63 No.1

<P>Summary</P><P>Plants recognize environmental factors to determine flowering time. <I>CONSTANS</I> (<I>CO</I>) plays a central role in the photoperiod flowering pathway of Arabidopsis, and CO protein stability is modulated by photoreceptors. In rice, <I>Hd1</I>, an ortholog of <I>CO</I>, acts as a flowering promoter, and phytochromes repress <I>Hd1</I> expression. Here, we investigated the functioning of <I>OsCOL4</I>, a member of the <I>CONSTANS-like</I> (<I>COL</I>) family in rice. <I>OsCOL4</I> null mutants flowered early under short or long days. In contrast, <I>OsCOL4</I> activation-tagging mutants (<I>OsCOL4-D</I>) flowered late in either environment. Transcripts of <I>Ehd1</I>, <I>Hd3a</I>, and <I>RFT1</I> were increased in the <I>oscol4</I> mutants, but reduced in the <I>OsCOL4-D</I> mutants. This finding indicates that <I>OsCOL4</I> is a constitutive repressor functioning upstream of <I>Ehd1.</I> By comparison, levels of <I>Hd1</I>, <I>OsID1</I>, <I>OsMADS50</I>, <I>OsMADS51</I>, and <I>OsMADS56</I> transcripts were not significantly changed in <I>oscol4</I> or <I>OsCOL4-D</I>, suggesting that <I>OsCOL4</I> functions independently from previously reported flowering pathways. In <I>osphyB</I> mutants, <I>OsCOL4</I> expression was decreased and <I>osphyB oscol4</I> double mutants flowered at the same time as the <I>osphyB</I> single mutants, indicating <I>OsCOL4</I> functions downstream of <I>OsphyB.</I> We also present evidence for two independent pathways through which OsPhyB controls flowering time. These pathways are: (i) night break-sensitive, which does not need <I>OsCOL4</I>; and (ii) night break-insensitive, in which <I>OsCOL4</I> functions between <I>OsphyB</I> and <I>Ehd1.</I></P>