The transcription factor SlHY5 regulates the ripening of tomato fruit at both the transcriptional and translational levels

AbstractLight plays a critical role in plant growth and development, but the mechanisms through which light regulates fruit ripening and nutritional quality in horticultural crops remain largely unknown. Here, we found that ELONGATED HYPOCOTYL 5 (HY5), a master regulator in the light signaling pathway, is required for normal fruit ripening in tomato (Solanum lycopersicum). Loss of function of tomato HY5 (SlHY5) impairs pigment accumulation and ethylene biosynthesis. Transcriptome profiling identified 2948 differentially expressed genes, which included 1424 downregulated and 1524 upregulated genes, in the Slhy5 mutants. In addition, genes involved in carotenoid and anthocyanin biosynthesis and ethylene signaling were revealed as direct targets of SlHY5 by chromatin immunoprecipitation. Surprisingly, the expression of a large proportion of genes encoding ribosomal proteins was downregulated in the Slhy5 mutants, and this downregulation pattern was accompanied by a decrease in the abundance of ribosomal proteins. Further analysis demonstrated that SlHY5 affected the translation efficiency of numerous ripening-related genes. These data indicate that SlHY5 regulates fruit ripening both at the transcriptional level by targeting specific molecular pathways and at the translational level by affecting the protein translation machinery. Our findings unravel the regulatory mechanisms of SlHY5 in controlling fruit ripening and nutritional quality and uncover the multifaceted regulation of gene expression by transcription factors.

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Suppression of Global Protein Translation in SARS-CoV-2 Infection

10.1101/2021.05.08.443207 ◽

2021 ◽

Author(s):

Haripriya Parthasarathy ◽

Divya Gupta ◽

Abhirami P Suresh ◽

Dixit Tandel ◽

Vishal Sah ◽

...

Keyword(s):

Ribosomal Proteins ◽

Critical Role ◽

Protein Translation ◽

Potential Contribution ◽

Strong Suppression ◽

Translational Machinery ◽

Polysome Profiling ◽

Viral Survival ◽

Global Translation ◽

Viral Titers

The relationship of SARS-CoV-2 with the host translation remains largely unexplored. Using polysome profiling of SARS-CoV-2 infected Caco2 cells, we here demonstrate that the virus induces a strong suppression of global translation by 48 hours of infection. Heavy polysome fractions displayed substantial depletion in the infected cells, indicating the loss of major translational activities in them. Further assessment of the major pathways regulating translation in multiple permissive cell lines revealed strong eIF4E dephosphorylation accompanied by Mnk1 depletion and ERK1/2 dephosphorylations. p38MAPK showed consistent activation and its inhibition lowered viral titers, indicating its importance in viral survival. No significant change was noticed in eIF2 α phosphorylation. mTORC1 pathway showed the most profound inhibition, indicating its potential contribution to the suppression of global translation associated with the infection. Pharmacological activation of mTORC1 caused a drop in viral titers while inhibition resulted in higher viral RNA levels, confirming a critical role of mTORC1 in regulating viral replication. Surprisingly, the infection did not cause a general suppression of 5′-TOP translation, as evident from the continued expression of ribosomal proteins. Our results collectively indicate that the differential suppression of mTORC1 might allow SARS-CoV-2 to hijack translational machinery in its favor and specifically target a set of host mRNAs.

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Microarray Gene Expression Analysis of Murine Tumor Heterogeneity Defined by Dynamic Contrast-Enhanced MRI

Molecular Imaging ◽

10.1162/15353500200202124 ◽

2002 ◽

Vol 1 (3) ◽

pp. 153535002002021

Author(s):

Nick G. Costouros ◽

Dominique Lorang ◽

Yantian Zhang ◽

Marshall S. Miller ◽

Felix E. Diehn ◽

...

Keyword(s):

Ribosomal Proteins ◽

Tumor Heterogeneity ◽

Protein Translation ◽

Pharmacokinetic Parameters ◽

Transcriptional Level ◽

Target Tissue ◽

Dce Mri ◽

Dynamic Contrast Enhanced ◽

Contrast Enhanced

Current methods of studying angiogenesis are limited in their ability to serially evaluate in vivo function throughout a target tissue. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and pharmacokinetic modeling provide a useful method for evaluating tissue vasculature based on contrast accumulation and washout. While it is often assumed that areas of high contrast enhancement and washout comprise areas of increased angiogenesis and tumor activity, the actual molecular pathways that are active in such areas are poorly understood. Using DCE-MRI in a murine subcutaneous tumor model, we were able to perform pharmacokinetic functional analysis of a tumor, coregistration of MRI images with histological cross-sections, immunohistochemistry, laser capture microdissection, and genetic profiling of tumor heterogeneity based on pharmacokinetic parameters. Using imaging as a template for biologic investigation, we have not found evidence of increased expression of proangiogenic modulators at the transcriptional level in either distinct pharmacokinetic region. Furthermore, these regions show no difference on histology and CD31 immunohistochemistry. However, the expression of ribosomal proteins was greatly increased in high enhancement and washout regions, implying increased protein translation and consequent increased cellular activity. Together, these findings point to the potential importance of posttranscriptional regulation in angiogenesis and the need for the development of angiogenesis-specific contrast agents to evaluate in vivo angiogenesis at a molecular level.

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A nuclear-localized cysteine desulfhydrase plays a role in fruit ripening in tomato

Horticulture Research ◽

10.1038/s41438-020-00439-1 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Kang-Di Hu ◽

Xiao-Yue Zhang ◽

Gai-Fang Yao ◽

Yu-Lei Rong ◽

Chen Ding ◽

...

Keyword(s):

Amino Acid ◽

Fruit Ripening ◽

Tomato Fruit ◽

Carotenoid Biosynthesis ◽

Ethylene Biosynthesis ◽

Chlorophyll Degradation ◽

Transcriptional Level ◽

Tomato Fruit Ripening ◽

Ethylene Signaling Pathway ◽

Cysteine Desulfhydrase

AbstractHydrogen sulfide (H2S) is a gaseous signaling molecule that plays multiple roles in plant development. However, whether endogenous H2S plays a role in fruit ripening in tomato is still unknown. In this study, we show that the H2S-producing enzyme l-cysteine desulfhydrase SlLCD1 localizes to the nucleus. By constructing mutated forms of SlLCD1, we show that the amino acid residue K24 of SlLCD1 is the key amino acid that determines nuclear localization. Silencing of SlLCD1 by TRV-SlLCD1 accelerated fruit ripening and reduced H2S production compared with the control. A SlLCD1 gene-edited mutant obtained through CRISPR/Cas9 modification displayed a slightly dwarfed phenotype and accelerated fruit ripening. This mutant also showed increased cysteine content and produced less H2S, suggesting a role of SlLCD1 in H2S generation. Chlorophyll degradation and carotenoid accumulation were enhanced in the SlLCD1 mutant. Other ripening-related genes that play roles in chlorophyll degradation, carotenoid biosynthesis, cell wall degradation, ethylene biosynthesis, and the ethylene signaling pathway were enhanced at the transcriptional level in the lcd1 mutant. Total RNA was sequenced from unripe tomato fruit treated with exogenous H2S, and transcriptome analysis showed that ripening-related gene expression was suppressed. Based on the results for a SlLCD1 gene-edited mutant and exogenous H2S application, we propose that the nuclear-localized cysteine desulfhydrase SlLCD1 is required for endogenous H2S generation and participates in the regulation of tomato fruit ripening.

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Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0624 ◽

2020 ◽

Vol 66 (9) ◽

pp. 521-528

Author(s):

Yanzi Xing ◽

Ruiqing Gong ◽

Yichun Xu ◽

Kunshan Liu ◽

Mian Zhou

Keyword(s):

Escherichia Coli ◽

Codon Usage ◽

Codon Usage Bias ◽

Cytosine Methylation ◽

Codon Optimization ◽

Mrna Level ◽

Protein Translation ◽

Transcriptional Level ◽

Translation Efficiency

Codon usage bias exists in almost every organism and is reported to regulate protein translation efficiency and folding. Besides translation, the preliminary role of codon usage bias on gene transcription has also been revealed in some eukaryotes such as Neurospora crassa. In this study, we took as an example the α-amylase-coding gene (amyA) and examined the role of codon usage bias in regulating gene expression in the typical prokaryote Escherichia coli. We confirmed the higher translation efficiency on codon-optimized amyA RNAs and found that the RNA level itself was also affected by codon optimization. The decreased RNA level was caused at least in part by altered mRNA stability at the post-transcriptional level. Codon optimization also altered the number of cytosine methylation sites. Examination on dcm knockouts suggested that cytosine methylation may be a minor mechanism adopted by codon bias to regulate gene RNA levels. More studies are required to verify the global effect of codon usage and to reveal its detailed mechanism on transcription.

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BiP is feed-back regulated by control of protein translation efficiency

Journal of Cell Science ◽

10.1242/jcs.115.11.2443 ◽

2002 ◽

Vol 115 (11) ◽

pp. 2443-2452 ◽

Cited By ~ 1

Author(s):

Karsten Gülow ◽

Detlef Bienert ◽

Ingrid G. Haas

Keyword(s):

Endoplasmic Reticulum ◽

Er Stress ◽

Protein Translation ◽

Transcriptional Level ◽

Translation Efficiency ◽

Transcript Levels ◽

Protein Levels ◽

Unfolded Protein ◽

Protein Response ◽

Translational Level

The lumenal endoplasmic reticulum (ER) protein BiP, among its other functions, is believed to serve as an ER stress sensor, triggering the so-called `unfolded protein response' or UPR. For this role, BiP levels are critical. Indeed, here we show that BiP expression is tightly controlled at a post-transcriptional level. Thus, an artificial increase in cellular BiP mRNA does not lead to increased synthesis of BiP in unstressed cells, and,consequently, protein levels remain constant. Under ER stress conditions,however, this homeostatic restriction is alleviated, and independent of transcript levels, the translation efficiency of BiP transcripts is enhanced,allowing the cells to produce more protein. We additionally show that this regulation is independent of elements in the 5′ and 3′ UTR of BiP mRNA, which rather points to a novel type of translational feedback control. BiP is the first example of a lumenal protein whose expression is controlled at a translational level. The implications of these findings with respect to cellular stress are discussed.

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The Small RNA Chaperone Hfq Is Required for the Virulence of Yersinia pseudotuberculosis

Infection and Immunity ◽

10.1128/iai.01046-09 ◽

2010 ◽

Vol 78 (5) ◽

pp. 2034-2044 ◽

Cited By ~ 63

Author(s):

Chelsea A. Schiano ◽

Lauren E. Bellows ◽

Wyndham W. Lathem

Keyword(s):

Yersinia Pseudotuberculosis ◽

Bacterial Species ◽

Critical Role ◽

Regulation Of Gene Expression ◽

Systemic Infection ◽

Protein Translation ◽

Effector Proteins ◽

Proper Function ◽

Mesenteric Lymph Nodes ◽

Protein Activity

ABSTRACT Bacterial small, noncoding RNAs (sRNAs) participate in the posttranscriptional regulation of gene expression, often by affecting protein translation, transcript stability, and/or protein activity. For proper function, many sRNAs rely on the chaperone Hfq, which mediates the interaction of the sRNA with its target mRNA. Recent studies have demonstrated that Hfq contributes to the pathogenesis of a number of bacterial species, suggesting that sRNAs play an essential role in the regulation of virulence. The enteric pathogen Yersinia pseudotuberculosis causes the disease yersiniosis. Here we show that Hfq is required by Y. pseudotuberculosis to cause mortality in an intragastric mouse model of infection, and a strain lacking Hfq is attenuated 1,000-fold compared to the wild type. Hfq is also required for virulence through the intraperitoneal route of infection and for persistence of the bacterium in the Peyer's patches, mesenteric lymph nodes, and spleen, suggesting a role for Hfq in systemic infection. Furthermore, the Δhfq mutant of Y. pseudotuberculosis is hypermotile and displays increased production of a biosurfactant-like substance, reduced intracellular survival in macrophages, and decreased production of type III secretion effector proteins. Together, these data demonstrate that Hfq plays a critical role in the virulence of Y. pseudotuberculosis by participating in the regulation of multiple steps in the pathogenic process and further highlight the unique role of Hfq in the virulence of individual pathogens.

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Regulation of gene expression during spermatogenesis at transcriptional level

Hereditas (Beijing) ◽

10.3724/sp.j.1005.2011.01300 ◽

2011 ◽

Vol 33 (12) ◽

pp. 1300-1307

Author(s):

Xiu-Jun ZHANG ◽

Mei-Ling LIU ◽

Meng-Chun JIA

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Transcriptional Level

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Recent Advances in the Function of the 67 kDa Laminin Receptor and its Targeting for Personalized Therapy in Cancer

Current Pharmaceutical Design ◽

10.2174/1381612823666170710125332 ◽

2017 ◽

Vol 23 (32) ◽

pp. 4745-4757 ◽

Cited By ~ 5

Author(s):

Ada Pesapane ◽

Pia Ragno ◽

Carmine Selleri ◽

Nunzia Montuori

Keyword(s):

Cell Adhesion ◽

Cancer Progression ◽

Ribosome Biogenesis ◽

Critical Role ◽

Protein Translation ◽

Basement Membranes ◽

Laminin Receptor ◽

Cell Surface Receptor ◽

Future Application ◽

Neoplastic Cells

The 67 kDa high affinity laminin receptor (67LR) is a non-integrin cell surface receptor for laminin, the major component of basement membranes. Interactions between 67LR and laminin play a major role in mediating cell adhesion, migration, proliferation and survival. 67LR derives from homo- or hetero-dimerization of a 37 kDa cytosolic precursor (37LRP), most probably by fatty acid acylation. Interestingly, 37LRP, also called p40 or OFA/iLR (oncofetal antigen/immature laminin receptor), is a multifunctional protein with a dual activity in the cytoplasm and in the nucleus. In the cytoplasm, 37LRP it is associated with the 40S subunit of ribosome, playing a critical role in protein translation and ribosome biogenesis while in the nucleus it is tightly associated with nuclear structures, and bound to components of the cytoskeleton, such as tubulin and actin. 67LR is mainly localized in the cell membrane, concentrated in lipid rafts. Acting as a receptor for laminin is not the only function of 67LR; indeed, it also acts as a receptor for viruses, bacteria and prions. 67LR expression is increased in neoplastic cells and correlates with an enhanced invasive and metastatic potential. The primary function of 67LR in cancer is to promote tumor cell adhesion to basement membranes, the first step in the invasion-metastasis cascade. Thus, 67LR is overexpressed in neoplastic cells as compared to their normal counterparts and its overexpression is considered a molecular marker of metastatic aggressiveness in cancer of many tissues, including breast, lung, ovary, prostate, stomach, thyroid and also in leukemia and lymphoma. Thus, inhibiting 67LR binding to laminin could be a feasible approach to block cancer progression. Here, we review the current understanding of the structure and function of this molecule, highlighting its role in cancer invasion and metastasis and reviewing the various therapeutic options targeting this receptor that could have a promising future application.

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RNA-binding proteins La and HuR cooperatively modulate translation repression of PDCD4 mRNA

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014894 ◽

2020 ◽

pp. jbc.RA120.014894

Author(s):

Ravi Kumar ◽

Dipak Kumar Poria ◽

Partho Sarothi Ray

Keyword(s):

Inflammatory Response ◽

Chronic Inflammation ◽

Rna Binding ◽

Rna Binding Proteins ◽

Critical Role ◽

Regulation Of Gene Expression ◽

Mrna Translation ◽

Suppressor Gene ◽

Cooperative Action ◽

Translation Repression

Post-transcriptional regulation of gene expression plays a critical role in controlling the inflammatory response. An uncontrolled inflammatory response results in chronic inflammation, often leading to tumorigenesis. Programmed cell death 4 (PDCD4) is a pro-inflammatory tumor-suppressor gene which helps to prevent the transition from chronic inflammation to cancer. PDCD4 mRNA translation is regulated by an interplay between the oncogenic microRNA miR-21 and the RNA-binding protein (RBP) HuR in response to LPS stimulation, but the role of other regulatory factors remain unknown. Here we report that the RBP Lupus antigen (La) interacts with the 3’UTR of PDCD4 mRNA and prevents miR-21-mediated translation repression. While LPS causes nuclear-cytoplasmic translocation of HuR, it enhances cellular La expression. Remarkably, La and HuR were found to bind cooperatively to the PDCD4 mRNA and mitigate miR-21-mediated translation repression. The cooperative action of La and HuR reduced cell proliferation and enhanced apoptosis, reversing the pro-oncogenic function of miR-21. Together, these observations demonstrate a cooperative interplay between two RBPs, triggered differentially by the same stimulus, which exerts a synergistic effect on PDCD4 expression and thereby helps maintain a balance between inflammation and tumorigenesis.

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Epigenetic Contribution and Genomic Imprinting Dlk1-Dio3 miRNAs in Systemic Lupus Erythematosus

Genes ◽

10.3390/genes12050680 ◽

2021 ◽

Vol 12 (5) ◽

pp. 680

Author(s):

Rujuan Dai ◽

Zhuang Wang ◽

S. Ansar Ahmed

Keyword(s):

Systemic Lupus Erythematosus ◽

Dna Methylation ◽

Lupus Erythematosus ◽

Critical Role ◽

Methylation Status ◽

Transcriptional Level ◽

Dna Hypomethylation ◽

Systemic Lupus ◽

Multiple Organs ◽

Genetic Imprinting

Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease that afflicts multiple organs, especially kidneys and joints. In addition to genetic predisposition, it is now evident that DNA methylation and microRNAs (miRNAs), the two major epigenetic modifications, are critically involved in the pathogenesis of SLE. DNA methylation regulates promoter accessibility and gene expression at the transcriptional level by adding a methyl group to 5′ cytosine within a CpG dinucleotide. Extensive evidence now supports the importance of DNA hypomethylation in SLE etiology. miRNAs are small, non-protein coding RNAs that play a critical role in the regulation of genome expression. Various studies have identified the signature lupus-related miRNAs and their functional contribution to lupus incidence and progression. In this review, the mutual interaction between DNA methylation and miRNAs regulation in SLE is discussed. Some lupus-associated miRNAs regulate DNA methylation status by targeting the DNA methylation enzymes or methylation pathway-related proteins. On the other hand, DNA hyper- and hypo-methylation are linked with dysregulated miRNAs expression in lupus. Further, we specifically discuss the genetic imprinting Dlk1-Dio3 miRNAs that are subjected to DNA methylation regulation and are dysregulated in several autoimmune diseases, including SLE.

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