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 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.

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.

scholarly journals The Arabidopsis thaliana MYB60 promoter provides a tool for the spatio-temporal control of gene expression in stomatal guard cells

2013 ◽  
Vol 64 (11) ◽  
pp. 3361-3371 ◽  
Author(s):  
Fabio Rusconi ◽  
Fabio Simeoni ◽  
Priscilla Francia ◽  
Eleonora Cominelli ◽  
Lucio Conti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Guard Cells ◽  
Temporal Control ◽  
Control Of Gene Expression ◽  
Stomatal Guard Cells ◽  
Spatio Temporal

scholarly journals The molecular dynamics of long noncoding RNA control of transcription in PTEN and its pseudogene

2017 ◽  
Vol 114 (37) ◽  
pp. 9942-9947 ◽  
Author(s):  
Nicholas Lister ◽  
Galina Shevchenko ◽  
James L. Walshe ◽  
Jessica Groen ◽  
Per Johnsson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Noncoding Rna ◽  
Dna Methyltransferase ◽  
Regulation Of Gene Expression ◽  
Control Of Gene Expression ◽  
Phosphatase And Tensin Homolog ◽  
Tensin Homolog ◽  
Sequence Components ◽  
Antisense Lncrnas

RNA has been found to interact with chromatin and modulate gene transcription. In human cells, little is known about how long noncoding RNAs (lncRNAs) interact with target loci in the context of chromatin. We find here, using the phosphatase and tensin homolog (PTEN) pseudogene as a model system, that antisense lncRNAs interact first with a 5′ UTR-containing promoter-spanning transcript, which is then followed by the recruitment of DNA methyltransferase 3a (DNMT3a), ultimately resulting in the transcriptional and epigenetic control of gene expression. Moreover, we find that the lncRNA and promoter-spanning transcript interaction are based on a combination of structural and sequence components of the antisense lncRNA. These observations suggest, on the basis of this one example, that evolutionary pressures may be placed on RNA structure more so than sequence conservation. Collectively, the observations presented here suggest a much more complex and vibrant RNA regulatory world may be operative in the regulation of gene expression.

scholarly journals Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

2009 ◽  
Vol 106 (17) ◽  
pp. 7028-7033 ◽  
Author(s):  
Zhe Ji ◽  
Ju Youn Lee ◽  
Zhenhua Pan ◽  
Bingjun Jiang ◽  
Bin Tian
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Posttranscriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Alternative Polyadenylation ◽  
Untranslated Regions ◽  
C2c12 Myoblast ◽  
Control Of Gene Expression ◽  
Differentiation And Proliferation

The 3′ untranslated regions (3′ UTRs) of mRNAs containcis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3′ UTRs as embryonic development progresses. This global regulation is controlled by alternative polyadenylation and coordinates with initiation of organogenesis and aspects of embryonic development, including morphogenesis, differentiation, and proliferation. Using myogenesis of C2C12 myoblast cells as a model, we recapitulated this process in vitro and found that 3′ UTR lengthening is likely caused by weakening of mRNA polyadenylation activity. Because alternative 3′ UTR sequences are typically longer and have higher AU content than constitutive ones, our results suggest that lengthening of 3′ UTR can significantly augment posttranscriptional control of gene expression during embryonic development, such as microRNA-mediated regulation.

Effect of Southern Root-knot Nematode (Meloidogyne incognita race 3) on Corn Yields in Alabama

2008 ◽  
Vol 9 (1) ◽  
pp. 11 ◽  
Author(s):  
K. L. Bowen ◽  
A. K. Hagan ◽  
H. L. Campbell ◽  
S. Nightengale
Keyword(s):  
Meloidogyne Incognita ◽  
Root Knot Nematode ◽  
Management Decisions ◽  
Root Knot Nematodes ◽  
Percent Loss ◽  
Stage Juvenile ◽  
Risk Thresholds ◽  
Southern Root Knot Nematode ◽  
Soil Losses ◽  
Corn Grain

In Alabama and other southeastern states, corn is frequently planted in rotation with cotton and peanut in order to minimize soil-borne pest problems. Even in areas where peanut is not grown, corn is increasingly being planted in rotation with cotton. However, one root-knot nematode, Meloidogyne incognita race 3, causes damage to both cotton and corn. In this study, we determined levels of corn grain loss when southern root-knot nematodes are present in soil. Losses were 3.8 to 11.4% based on preceding years' counts and 2.2 to 7.0% with current years' counts for every 100 2nd-stage juvenile root-knot nematodes in 100 cm ≥ of soil. Knowledge of the percent loss in corn grain due to southern rootknot nematode populations can provide additional guidance for use of risk thresholds when growers are making management decisions. Accepted for publication 21 June 2008. Published 10 September 2008.

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