scholarly journals Meeting at the DNA: Specifying Cytokinin Responses through Transcription Factor Complex Formation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1458
Author(s):  
Jan Erik Leuendorf ◽  
Thomas Schmülling
Keyword(s):  
Plant Hormone ◽  
Target Genes ◽  
Response Regulator ◽  
Biological Processes ◽  
Type B ◽  
Cytokinin Signaling ◽  
Expression Control ◽  
Cytokinin Response ◽  
Transcription Factor Complex ◽  
Targeted Approach

Cytokinin is a plant hormone regulating numerous biological processes. Its diverse functions are realized through the expression control of specific target genes. The transcription of the immediate early cytokinin target genes is regulated by type-B response regulator proteins (RRBs), which are transcription factors (TFs) of the Myb family. RRB activity is controlled by phosphorylation and protein degradation. Here, we focus on another step of regulation, the interaction of RRBs among each other or with other TFs to form active or repressive TF complexes. Several examples in Arabidopsis thaliana illustrate that RRBs form homodimers or complexes with other TFs to specify the cytokinin response. This increases the variability of the output response and provides opportunities of crosstalk between the cytokinin signaling pathway and other cellular signaling pathways. We propose that a targeted approach is required to uncover the full extent and impact of RRB interaction with other TFs.

scholarly journals The Type-B Cytokinin Response Regulator ARR1 Inhibits Shoot Regeneration in an ARR12-Dependent Manner in Arabidopsis

2020 ◽  
Vol 32 (7) ◽  
pp. 2271-2291 ◽  
Author(s):  
Zhenhua Liu ◽  
Xuehuan Dai ◽  
Juan Li ◽  
Na Liu ◽  
Xiangzheng Liu ◽  
...  
Keyword(s):  
Shoot Regeneration ◽  
Response Regulator ◽  
Dependent Manner ◽  
Type B ◽  
Cytokinin Response

scholarly journals A Cytokinin Signaling Type-B Response Regulator Transcription Factor Acting in Early Nodulation

2020 ◽  
Vol 183 (3) ◽  
pp. 1319-1330 ◽  
Author(s):  
Sovanna Tan ◽  
Myriam Sanchez ◽  
Carole Laffont ◽  
Stéphane Boivin ◽  
Christine Le Signor ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Response Regulator ◽  
Type B ◽  
Cytokinin Signaling

Genome-Wide Identification and Analysis of the Type-B Authentic Response Regulator Gene Family in Peach (Prunus persica)

2017 ◽  
Vol 151 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Jingjue Zeng ◽  
Xudong Zhu ◽  
Muhammad S. Haider ◽  
Xicheng Wang ◽  
Cheng Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Response Regulator ◽  
Expression Profiles ◽  
Protein Domain ◽  
Future Research ◽  
Type B ◽  
Cytokinin Signaling ◽  
Peach Genome

The type-B authentic response regulator (ARR-B) family members serve as DNA-binding transcriptional regulators, whose activities are probably regulated by phosphorylation/dephosphorylation, resulting in the rapid induction of type-A ARR genes. Type-B ARRs are believed to be involved in many biological processes, including cytokinin signaling, plant growth, and stress responses through a chaperone or by isomerization of proline residues during protein folding. The public availability of complete peach genome sequences allows the identification of 23 ARR-B genes by HMMER and blast analysis. Scaffold locations of these genes in the peach genome were determined, and the protein domain and motif organization of peach type-B ARRs were analyzed. The phylogenetic relationships between peach type-B ARRs were also assessed. The expression profiles of peach ARR-B genes revealed that most of the type-B ARRs showed high expression levels in tissues undergoing rapid cell division and may engage more cytokinins, like half-opened flowers, fruits at expansion stages, and young leaves. These findings not only contribute to a better understanding of the complex regulation of the peach ARR-B gene family, but also provide valuable information for future research in peach functional genomics.

Feeding behaviour and bioerosion: the ecological role of the rock-boring urchin, Echinometra mathaei (de Blainville, 1825), in Okinawa reef flat

2013 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Noar Muda Satyawan ◽  
Shelly Tutupoho ◽  
Yusli Wardiatno ◽  
Makoto Tsuchiya
Keyword(s):  
Feeding Behaviour ◽  
Reef Flat ◽  
Type A ◽  
Gut Contents ◽  
Biological Processes ◽  
Type B ◽  
Night Time ◽  
Echinometra Mathaei ◽  
Benthic Ecosystems

Erosion rate on corals due to activities of other biota is called bioerosion. The rock-boring urchin, Echinometra mathaei, when it is abundant, plays a significant role in benthic ecosystems, including biological processes like coral erosion. During feeding, E. mathaei erodes calcium carbonate besides grazing on algae living on coral, so it plays an important role in both organic and inorganic carbons in coral reefs. The urchin E. mathaei actively feeds during the night time (nocturnal grazer). Although in Okinawa four types (A-D) of the urchin exist, the research only focused on the types A and B. Type A of E. mathaei produced 0.44951 g feces per day on average while type B produced 0.38030 g feces per day. CaCO3 analysis in feces and gut contents showed bioerosion rate of E. mathaei type A was 0.64492 g/individu/day, and 0.54436 g/individu/day in type B. There were no significant differences in bioerosion impact of E. mathaei type A and B© Laju erosi pada karang yang disebabkan oleh biota, dikenal dengan bioerosi. Bulu babi jenis Echinometra mathaei, ketika melimpah, menjadi sangat berpengaruh terhadap ekosistem bentik termasuk proses biologi seperti erosi karang. Selama aktivitas makan, E. mathaei menggerus kalsium karbonat dalam proporsi yang besar di samping alga yang tumbuh menempel pada karang sehingga memiliki peran penting dalam siklus karbon organik dan anorganik di ekosistem terumbu karang. Bulu babi E. mathaei aktif mencari makan pada malam hari (nocturnal grazer). Meskipun di Okinanawa ada 4 tipe (A-D), pada eksperimen kali ini memfokuskan pada tipe A dan B saja. Tipe A E. mathaei rata-rata memproduksi 0,44951 g feses/hari dan tipe B memproduksi 0,38030 g feses/hari. Berdasarkan analisis CaCO3 yang dilakukan pada feses dan isi lambung, laju bioerosi yang disebabkan oleh E. mathaei tipe A sebesar 0,64492 g/individu/hari sedangkan tipe B sebesar 0,54436 g/individu/hari. Tidak terdapat perbedaan dampak bioerosi yang signifikan antara E. mathaei tipe A dan B©

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

scholarly journals Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Bo Chen ◽  
Huimin Xu ◽  
Yayu Guo ◽  
Paul Grünhofer ◽  
Lukas Schreiber ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormone ◽  
Target Genes ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Vascular Cambium ◽  
Differentially Methylated Region ◽  
Gene Body Methylation ◽  
Transcription Analysis ◽  
Global Methylation

AbstractTrees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium in Populus tomentosa during the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.

scholarly journals The Relationship between AGAMOUS and Cytokinin Signaling in the Establishment of Carpeloid Features

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 827
Author(s):  
Andrea Gómez-Felipe ◽  
Daniel Kierzkowski ◽  
Stefan de Folter
Keyword(s):  
Regulatory Network ◽  
Dependent Manner ◽  
Mads Box ◽  
Type B ◽  
Cytokinin Signaling ◽  
Reproductive Structures ◽  
Carpel Development ◽  
Gene Regulatory ◽  
The Relationship ◽  
Gynoecium Development

Gynoecium development is dependent on gene regulation and hormonal pathway interactions. The phytohormones auxin and cytokinin are involved in many developmental programs, where cytokinin is normally important for cell division and meristem activity, while auxin induces cell differentiation and organ initiation in the shoot. The MADS-box transcription factor AGAMOUS (AG) is important for the development of the reproductive structures of the flower. Here, we focus on the relationship between AG and cytokinin in Arabidopsis thaliana, and use the weak ag-12 and the strong ag-1 allele. We found that cytokinin induces carpeloid features in an AG-dependent manner and the expression of the transcription factors CRC, SHP2, and SPT that are involved in carpel development. AG is important for gynoecium development, and contributes to regulating, or else directly regulates CRC, SHP2, and SPT. All four genes respond to either reduced or induced cytokinin signaling and have the potential to be regulated by cytokinin via the type-B ARR proteins. We generated a model of a gene regulatory network, where cytokinin signaling is mainly upstream and in parallel with AG activity.

scholarly journals Emerging multifaceted roles of BAP1 complexes in biological processes

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Aileen Patricia Szczepanski ◽  
Lu Wang
Keyword(s):  
Transcriptional Repression ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Multiprotein Complex ◽  
Downstream Target ◽  
Evolutionarily Conserved ◽  
Complex Forms ◽  
Polycomb Repressive Complex 1

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

Dynamical Analysis of bantam-Regulated Drosophila Circadian Rhythm Model

2014 ◽  
Vol 24 (12) ◽  
pp. 1450161 ◽  
Author(s):  
Ying Li ◽  
Zengrong Liu
Keyword(s):  
Circadian Rhythm ◽  
Crucial Role ◽  
Target Genes ◽  
Classical Model ◽  
Dynamical Analysis ◽  
Biological Processes ◽  
Biological Mechanisms ◽  
Environmental Perturbations ◽  
Dynamical Behaviors ◽  
Important Regulator

MicroRNAs (miRNAs) interact with 3′untranslated region (UTR) elements of target genes to regulate mRNA stability or translation, and play a crucial role in regulating many different biological processes. bantam, a conserved miRNA, is involved in several functions, such as regulating Drosophila growth and circadian rhythm. Recently, it has been discovered that bantam plays a crucial role in the core circadian pacemaker. In this paper, based on experimental observations, a detailed dynamical model of bantam-regulated circadian clock system is developed to show the post-transcriptional behaviors in the modulation of Drosophila circadian rhythm, in which the regulation of bantam is incorporated into a classical model. The dynamical behaviors of the model are consistent with the experimental observations, which shows that bantam is an important regulator of Drosophila circadian rhythm. The sensitivity analysis of parameters demonstrates that with the regulation of bantam the system is more sensitive to perturbations, indicating that bantam regulation makes it easier for the organism to modulate its period against the environmental perturbations. The effectiveness in rescuing locomotor activity rhythms of mutated flies shows that bantam is necessary for strong and sustained rhythms. In addition, the biological mechanisms of bantam regulation are analyzed, which may help us more clearly understand Drosophila circadian rhythm regulated by other miRNAs.

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