Abstract
Leaves provide energy for plants, and consequently for animals, through photosynthesis. Despite their important functions, plant leaf developmental processes and their underlying mechanisms ...have not been well characterized. Here, we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling functions. Cytokinins maintain the growth potential (pluripotency) of shoot apical meristems, which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation; cytokinins and auxins, as well as their interaction, determine the phyllotaxis pattern. The activities of cytokinins in various regions of the leaf, especially at the margins, collectively determine the final leaf morphology (e.g., simple or compound). The area of a leaf is generally determined by the number and size of the cells in the leaf. Cytokinins promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development, respectively. During leaf senescence, cytokinins reduce sugar accumulation, increase chlorophyll synthesis, and prolong the leaf photosynthetic period. We also briefly describe the roles of other hormones, including auxin and ethylene, during the whole leaf developmental process. In this study, we review the regulatory roles of cytokinins in various leaf developmental stages, with a focus on cytokinin metabolism and signal transduction processes, in order to shed light on the molecular mechanisms underlying leaf development.
Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited ...information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.
In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).
The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors ...(ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35
genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures,
-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these
genes and revealed that 16 of them, including
,
,
,
,
-
,
,
,
,
,
,
, and
, were preferentially expressed in primary stems, while 15 of them, including
,
,
,
,
,
,
-
,
,
,
,
,
, and
, participated in different phases of wood formation. In addition, some
genes, with at least one
-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the
gene family, which will lay some foundation for future research about
genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
Phytoplasmas are cell wall-less bacteria that induce abnormal plant growth and various diseases, causing severe economic loss. Phytoplasmas are highly dependent on nutrients imported from host cells ...because they have lost many genes involved in essential metabolic pathways during reductive evolution. However, metabolic crosstalk between phytoplasmas and host plants and the mechanisms of phytoplasma nutrient acquisition remain poorly understood. In this study, using metabolomics approach, sweet cherry virescence (SCV) phytoplasma-induced metabolite alterations in sweet cherry trees were investigated. A total of 676 metabolites were identified in SCV phytoplasma-infected and mock inoculated leaves, of which 187 metabolites were differentially expressed, with an overwhelming majority belonging to carbohydrates, fatty acids/lipids, amino acids, and flavonoids. Available omics data of interactions between plant and phytoplasma were also deciphered and integrated into the present study. The results demonstrated that phytoplasma infection promoted glycolysis and pentose phosphate pathway activities, which provide energy and nutrients, and facilitate biosynthesis of necessary low-molecular metabolites. Our findings indicated that phytoplasma can induce reprograming of plant metabolism to obtain nutrients for its own replication and infection. The findings from this study provide new insight into interactions of host plants and phytoplasmas from a nutrient acquisition perspective.
Epigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. ...Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.
Present knowledge indicates a multilayered hierarchical gene regulatory network (ML-hGRN) often operates above a biological pathway. Although the ML-hGRN is very important for understanding how a ...pathway is regulated, there is almost no computational algorithm for directly constructing ML-hGRNs.
A backward elimination random forest (BWERF) algorithm was developed for constructing the ML-hGRN operating above a biological pathway. For each pathway gene, the BWERF used a random forest model to calculate the importance values of all transcription factors (TFs) to this pathway gene recursively with a portion (e.g. 1/10) of least important TFs being excluded in each round of modeling, during which, the importance values of all TFs to the pathway gene were updated and ranked until only one TF was remained in the list. The above procedure, termed BWERF. After that, the importance values of a TF to all pathway genes were aggregated and fitted to a Gaussian mixture model to determine the TF retention for the regulatory layer immediately above the pathway layer. The acquired TFs at the secondary layer were then set to be the new bottom layer to infer the next upper layer, and this process was repeated until a ML-hGRN with the expected layers was obtained.
BWERF improved the accuracy for constructing ML-hGRNs because it used backward elimination to exclude the noise genes, and aggregated the individual importance values for determining the TFs retention. We validated the BWERF by using it for constructing ML-hGRNs operating above mouse pluripotency maintenance pathway and Arabidopsis lignocellulosic pathway. Compared to GENIE3, BWERF showed an improvement in recognizing authentic TFs regulating a pathway. Compared to the bottom-up Gaussian graphical model algorithm we developed for constructing ML-hGRNs, the BWERF can construct ML-hGRNs with significantly reduced edges that enable biologists to choose the implicit edges for experimental validation.
Drought stress causes various negative impacts on plant growth and crop production. R2R3-MYB transcription factors (TFs) play crucial roles in the response to abiotic stress. However, their functions ...in
haven't been fully investigated. In this study, a R2R3 MYB transcription factor gene,
, was identified from
and reveals its significant role in drought stress. Overexpression of
enhances tolerance to drought stress in contrast to repression of
by RNA interference (RNAi) in transgenic experiment. The overexpression lines increased peroxidase (POD) and superoxide dismatase (SOD) activities, while decreased hydrogen peroxide (H
O
), superoxide radicals (O
), electrolyte leakage (EL) and malondialdehyde (MDA) contents. Our study showed that overexpression of
increased
gene expression up to 20-fold due to BpMYB123 directly binding to the MYB1AT element of
promoter. These results indicate that BpMYB123 acts as a regulator via regulating
to improve drought tolerance in birch.
Background & Aims We studied the functions of natural killer (NK) cells and the role of the NK cell inhibitory receptor (NKG2A) during hepatitis B virus (HBV) infection in patients and mice. Methods ...We analyzed levels of NKG2A on peripheral blood NK cells from 42 patients with active chronic hepatitis B (CHB), 31 patients with inactive CHB, and 35 healthy volunteers (controls). Five patients with CHB treated with antiviral therapy were also included to evaluate changes in NK cells after HBV titers decreased. We examined the effects of blocking antibodies against NKG2A or its ligand Qa-1 (equivalent to HLA-E in humans) in immunocompetent mice that express HBV from a plasmid and are positive for serum hepatitis B surface antigen (a mouse model of HBV infection). Results A higher percentage of NK cells from patients with active CHB were positive for NKG2A (38.47%) than from patients with inactive CHB (19.33%; P < .01) or controls (27.96%; P < .05). The percentage of NKG2A+ cells correlated with serum viral load ( r = 0.5457; P < .001). The percentage of NKG2A+ cells decreased along with HBV load in patients that received antiviral therapy ( P < .05). Blocking NKG2A interaction with HLA-E in peripheral NK cells from patients with active CHB increased their cytotoxicity in vitro. NK cells of HBV carrier mice also had higher percentages of NK cells that expressed NKG2A compared with control mice; NKG2A was likely to be up-regulated by production of interleukin-10 by hepatic regulatory CD4+ CD25+ T cells. Blocking Qa-1 in these mice promoted viral clearance in an NK cell−dependent manner. Conclusions Infection with HBV increases levels of the inhibitory receptor NKG2A on NK cells in mice and humans, and reduces their ability to clear HBV. Reagents designed to block the interaction between NKG2A and HLA-E might be developed to treat CHB infection.
The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and ...developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.
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