scholarly journals Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes

2021 ◽  
Author(s):  
Martine Da Rocha ◽  
Caroline Bournaud ◽  
Julie Dazeniere ◽  
Peter Thorpe ◽  
Clement Pellegrin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Meloidogyne Incognita ◽  
Life Stage ◽  
Regulation Of Gene Expression ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Control Of Gene Expression ◽  
Precise Control ◽  
Effector Genes ◽  
Spatio Temporal

Root-knot nematodes are the major contributor to the crop losses caused by nematodes. Root-knot nematodes secrete effectors into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effectors. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands: providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus and termed it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode, and identify a new set of candidate effector genes that will guide future functional analyses.

scholarly journals Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 771
Author(s):  
Martine Da Rocha ◽  
Caroline Bournaud ◽  
Julie Dazenière ◽  
Peter Thorpe ◽  
Marc Bailly-Bechet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Meloidogyne Incognita ◽  
Life Stage ◽  
Regulation Of Gene Expression ◽  
Effector Proteins ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Control Of Gene Expression ◽  
Effector Genes ◽  
Spatio Temporal

Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.

scholarly journals Removal of H3K27me3 by JMJ Proteins Controls Plant Development and Environmental Responses in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Nobutoshi Yamaguchi
Keyword(s):  
Gene Expression ◽  
Plant Development ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Histone H3 ◽  
Control Of Gene Expression ◽  
Precise Control ◽  
Repressive Histone Modification ◽  
Environmental Responses

Trimethylation of histone H3 lysine 27 (H3K27me3) is a highly conserved repressive histone modification that signifies transcriptional repression in plants and animals. In Arabidopsis thaliana, the demethylation of H3K27 is regulated by a group of JUMONJI DOMAIN-CONTANING PROTEIN (JMJ) genes. Transcription of JMJ genes is spatiotemporally regulated during plant development and in response to the environment. Once JMJ genes are transcribed, recruitment of JMJs to target genes, followed by demethylation of H3K27, is critically important for the precise control of gene expression. JMJs function synergistically and antagonistically with transcription factors and/or other epigenetic regulators on chromatin. This review summarizes the latest advances in our understanding of Arabidopsis H3K27me3 demethylases that provide robust and flexible epigenetic regulation of gene expression to direct appropriate development and environmental responses in plants.

scholarly journals Nutritional Regulation of Gene Expression: Carbohydrate-, Fat- and Amino Acid-Dependent Modulation of Transcriptional Activity

2019 ◽  
Vol 20 (6) ◽  
pp. 1386 ◽  
Author(s):  
Diego Haro ◽  
Pedro Marrero ◽  
Joana Relat
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Regulation Of Gene Expression ◽  
Peroxisome Proliferator ◽  
Nutritional Regulation ◽  
Control Of Gene Expression ◽  
Nutritional Interventions ◽  
Precise Control

The ability to detect changes in nutrient levels and generate an adequate response to these changes is essential for the proper functioning of living organisms. Adaptation to the high degree of variability in nutrient intake requires precise control of metabolic pathways. Mammals have developed different mechanisms to detect the abundance of nutrients such as sugars, lipids and amino acids and provide an integrated response. These mechanisms include the control of gene expression (from transcription to translation). This review reports the main molecular mechanisms that connect nutrients’ levels, gene expression and metabolism in health. The manuscript is focused on sugars’ signaling through the carbohydrate-responsive element binding protein (ChREBP), the role of peroxisome proliferator-activated receptors (PPARs) in the response to fat and GCN2/activating transcription factor 4 (ATF4) and mTORC1 pathways that sense amino acid concentrations. Frequently, alterations in these pathways underlie the onset of several metabolic pathologies such as obesity, insulin resistance, type 2 diabetes, cardiovascular diseases or cancer. In this context, the complete understanding of these mechanisms may improve our knowledge of metabolic diseases and may offer new therapeutic approaches based on nutritional interventions and individual genetic makeup.

scholarly journals Precise tuning of gene expression output levels in mammalian cells

2018 ◽  
Author(s):  
Yale S. Michaels ◽  
Mike B. Barnkob ◽  
Hector Barbosa ◽  
Toni A. Baeumler ◽  
Mary K. Thompson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
Regulation Of Gene Expression ◽  
Antigen Expression ◽  
Control Of Gene Expression ◽  
Precise Control ◽  
Mouse Melanoma Model

ABSTRACTPrecise, analogue regulation of gene expression is critical for development, homeostasis and regeneration in mammals. In contrast, widely employed experimental and therapeutic approaches such as knock-in/out strategies are more suitable for binary control of gene activity, while RNA interference (RNAi) can lead to pervasive off-target effects and unpredictable levels of repression. Here we report on a method for the precise control of gene expression levels in mammalian cells based on engineered, synthetic microRNA response elements (MREs). To develop this system, we established a high-throughput sequencing approach for measuring the efficacy of thousands of miR-17 MRE variants. This allowed us to create a library of microRNA silencing-mediated fine-tuners (miSFITs) of varying strength that can be employed to control the expression of user specified genes. To demonstrate the value of this technology, we used a panel of miSFITs to tune the expression of a peptide antigen in a mouse melanoma model. This analysis revealed that antigen expression level is a key determinant of the anti-tumour immune response in vitro and in vivo. miSFITs are a powerful tool for modulating gene expression output levels with applications in research and cellular engineering.

Single pass cDNA sequencing - a powerful tool to analyse gene expression in preparasitic juveniles of the southern root-knot nematode Meloidogyne incognita

Nematology ◽  
2001 ◽  
Vol 3 (2) ◽  
pp. 129-139 ◽  
Author(s):  
Jaap Bakker ◽  
Fred Gommers ◽  
Geert Smant ◽  
Pierre Abad ◽  
Marie-Noëlle Rosso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cdna Library ◽  
Meloidogyne Incognita ◽  
Sequence Data ◽  
Homo Sapiens ◽  
Large Fraction ◽  
Nematode Species ◽  
Cdna Libraries ◽  
Parasitic Nematodes ◽  
Root Knot Nematode

AbstractExpressed sequence tags (EST) have been widely used to assist in gene discovery in various organisms (e.g., Arabidopsis thaliana, Caenorhabditis elegans, Mus musculus, and Homo sapiens). In this paper we describe an EST project, which aims to investigate gene expression in Meloidogyne incognita at the onset of parasitism. Approximately 1000 5′-end sequence tags were produced from a cDNA library made of freshly hatched preparasitic second stage juveniles (J2). The EST were identified in the primary transformants of the cDNA library, and assigned to nine different functional groups, including (candidate) parasitism genes. A large fraction of the EST (45%) did not have a putative homologue in public databases. Sixty five percent of the EST that could be clustered into a functional group had putative homologues in other nematode species. EST were found for virtually all parasitism related genes that have been cloned from M. incognita to date. In addition, several novel genes were tagged, including a xylanase and a chitinase gene. The efficiency of EST projects, which produce sequence data for thousands of genes in months time without any difficult pre-selections of mRNA pools, makes random sequencing cDNA libraries a superior method to identify candidates for parasitism related genes in plant-parasitic nematodes. The sequences in this paper are retrievable from Genbank with the accession numbers BE191640 to BE191741, BE217592 to BE217720, BE225324 to BE225598, BE238852 to BE239221, and BE240829 to BE240865.

scholarly journals Regulatory signals in messenger RNA: determinants of nutrient–gene interaction and metabolic compartmentation

1998 ◽  
Vol 80 (4) ◽  
pp. 307-321
Author(s):  
John E. Hesketh ◽  
M. Helena Vasconcelos ◽  
Giovanna Bermano
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Mrna Stability ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Untranslated Regions ◽  
Nutritional Requirements ◽  
Control Of Gene Expression ◽  
Metabolic Compartmentation ◽  
Post Transcriptional Regulation

Nutrition has marked influences on gene expression and an understanding of the interaction between nutrients and gene expression is important in order to provide a basis for determining the nutritional requirements on an individual basis. The effects of nutrition can be exerted at many stages between transcription of the genetic sequence and production of a functional protein. This review focuses on the role of post-transcriptional control, particularly mRNA stability, translation and localization, in the interactions of nutrients with gene expression. The effects of both macronutrients and micronutrients on regulation of gene expression by post-transcriptional mechanisms are presented and the post-transcriptional regulation of specific genes of nutritional relevance (glucose transporters, transferrin, selenoenzymes, metallothionein, lipoproteins) is described in detail. The function of the regulatory signals in the untranslated regions of the mRNA is highlighted in relation to control of mRNA stability, translation and localization and the importance of these mRNA regions to regulation by nutrients is illustrated by reference to specific examples. The localization of mRNA by signals in the untranslated regions and its function in the spatial organization of protein synthesis is described; the potential of such mechanisms to play a key part in nutrient channelling and metabolic compartmentation is discussed. It is concluded that nutrients can influence gene expression through control of the regulatory signals in these untranslated regions and that the post-transcriptional regulation of gene expression by these mechanisms may influence nutritional requirements. It is emphasized that in studies of nutritional control of gene expression it is important not to focus only on regulation through gene promoters but also to consider the possibility of post-transcriptional control.

scholarly journals Application of Biogas Digestate with Rice Straw Mitigates Nitrate Leaching Potential and Suppresses Root-Knot Nematode (Meloidogyne incognita)

Agronomy ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 227 ◽  
Author(s):  
Yuexi Wang ◽  
Seiya Chikamatsu ◽  
Tuya Gegen ◽  
Kozue Sawada ◽  
Koki Toyota ◽  
...  
Keyword(s):  
Rice Straw ◽  
Nitrate Leaching ◽  
Meloidogyne Incognita ◽  
Application Rate ◽  
Pig Manure ◽  
Test Plant ◽  
Root Knot Nematode ◽  
Root Knot Nematodes ◽  
Leaching Potential ◽  
Biogas Digestate

This study investigated the effects of biogas digestate application to soil with rice straw on nitrate leaching potential and nematicidal activity toward root-knot nematodes Meloidogyne incognita. The following seven treatments were set up: (i) control (CONT); (ii) chemical fertilizer (CF); (iii) wet biogas digestate derived from pig manure (WBD); (iv) and (v) dry biogas digestate derived from a mixture of pig manure and rice straw at an initial C/N ratio of 20 and 30 (DBD20 and DBD30); (vi) and (vii) DBD20 mixed with rice straw to adjust the C/N ratio to 16 (Mix1) and 30 (Mix2), respectively. The application rate of CF and digestates was adjusted to 200 mg N kg−1 soil based on the inorganic ammonium nitrogen contents. Nitrate contents readily increased in all the treatments with incubation, except for Mix2, and those at day 90 were decreased with increasing initial labile C contents. Garden balsam was grown as a test plant for root-knot nematodes using the soils at day 90 and the results showed that the gall index was significantly lower in Mix2 and Mix1 than in CF. These results suggest that dry digestate mixed with rice straw might have potential for lower nitrate leaching and nematicidal properties.

Comparison of host recognition, invasion, development and reproduction of Meloidogyne graminicola and M. incognita on rice and tomato

Nematology ◽  
2011 ◽  
Vol 13 (5) ◽  
pp. 509-520 ◽  
Author(s):  
Tushar K. Dutta ◽  
Stephen J. Powers ◽  
Brian R. Kerry ◽  
Hari S. Gaur ◽  
Rosane H.C. Curtis
Keyword(s):  
Meloidogyne Incognita ◽  
Host Recognition ◽  
Cortical Region ◽  
Root Knot Nematode ◽  
Root Tips ◽  
Root Knot Nematodes ◽  
Tomato Plants ◽  
Meloidogyne Graminicola ◽  
Second Stage ◽  
Tomato Roots

AbstractThe rice root-knot nematode Meloidogyne graminicola normally infects rice, wheat and several other graminaceous plants. Meloidogyne incognita is a serious pest of dicotyledonous crops, although it can infect and reproduce on some cereals. This paper demonstrates and compares host recognition, development and reproduction of these two species of root-knot nematodes on rice and tomato plants. Attraction bioassays in pluronic gel clearly showed that M. incognita preferred tomato roots to rice or mustard roots, whilst M. graminicola was more attracted towards rice compared with tomato or mustard roots. Based on the attraction data from this study, it can be hypothesised that either: i) the blend of attractants and repellents are different in good and poor hosts; or ii) relatively long-range attractants, together with shorter-range repellents, might affect nematode movement patterns. Some host specific attractants might also be involved. Meloidogyne incognita was able to invade and develop to adult female but did not produce eggs in rice roots. By contrast, M. graminicola developed and reproduced faster on both rice and tomato plants compared with M. incognita. Nevertheless, second-stage juveniles of both these root-knot nematodes showed a similar pattern of distribution inside the roots, preferring to accumulate at the root tips of rice or in the vascular cylinder and cortical region of tomato.

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