CLE peptide tri-arabinosylation and peptide domain sequence composition are essential for SUNN-dependent autoregulation of nodulation inMedicago truncatula

AbstractLegume plants form a symbiosis with N2-fixing soil rhizobia, resulting in new root organs called nodules that enable N2-fixation. Nodulation is a costly process that is tightly regulated by the host through Autoregulation of Nodulation (AON) and nitrate-dependent regulation of nodulation. Both pathways require legume-specific CLAVATA/ESR-related (CLE) peptides. Nitrogen-induced nodulation-suppressing CLE peptides have not previously been characterised in Medicago truncatula, with only rhizobia-induced MtCLE12 and MtCLE13 identified. Here, we report on novel peptides MtCLE34 and MtCLE35 in nodulation control pathways. The nodulation-suppressing CLE peptides of five legume species were classified into three clades based on sequence homology and phylogeny. This approached identified MtCLE34 and MtCLE35 and four new CLE peptide orthologues of Pisum sativum. Whereas MtCLE12 and MtCLE13 are induced by rhizobia, MtCLE34 and MtCLE35 respond to both rhizobia and nitrate. MtCLE34 was identified as a pseudogene lacking a functional CLE-domain. Overexpression of MtCLE12, MtCLE13 and MtCLE35 inhibits nodulation. Together, our findings indicate that MtCLE12 and MtCLE13 have a distinct role in AON, while MtCLE35 regulates nodule numbers in a rhizobia- and nitrate-dependent manner. MtCLE34 likely had a similar role to MtCLE35 but its function was lost due to a nonsense mutation resulting in the loss of the mature peptide.

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Shoot-derived miR2111 controls legume root and nodule development

10.1101/2020.09.02.278739 ◽

2020 ◽

Cited By ~ 1

Author(s):

Mengbai Zhang ◽

Huanan Su ◽

Peter M. Gresshoff ◽

Brett J. Ferguson

Keyword(s):

Lateral Root ◽

Lateral Roots ◽

Ectopic Expression ◽

Root System Architecture ◽

Negative Regulator ◽

Nodule Development ◽

Wild Type ◽

Root Branching ◽

Autoregulation Of Nodulation ◽

Cle Peptide

AbstractLegumes control their nodule numbers through the Autoregulation Of Nodulation (AON). Rhizobia infection stimulates the production of root-derived CLE peptide hormones that are translocated to the shoot where they regulate a new signal. We used soybean to demonstrate that this shoot-derived signal is miR2111, which is transported via phloem to the root where it targets transcripts of Too Much Love (TML), a negative regulator of nodulation. Shoot perception of rhizobia-induced CLE peptides suppresses miR2111 expression, resulting in TML accumulation in roots and subsequent inhibition of nodule organogenesis. Feeding synthetic mature miR2111 via the petiole increased nodule numbers per plant. Likewise, elevating miR2111 availability by over-expression promoted nodulation, while target mimicry of TML induced the opposite effect on nodule development in wild-type plants and alleviated the supernodulating and stunted root growth phenotypes of AON-defective mutants. Additionally, in non-nodulating wild-type plants, ectopic expression of miR2111 significantly enhanced lateral root emergence with a decrease in lateral root length and average root diameter. In contrast, hairy roots constitutively expressing the target mimic construct exhibited reduced lateral root density. Overall, these findings demonstrate that miR2111 is both the critical shoot-to-root factor that positively regulates root nodule development, and also acts to shape root system architecture via orchestrating the degree of root branching, as well as the length and thickness of lateral roots.

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The structure and activity of nodulation-suppressing CLE peptide hormones of legumes

Functional Plant Biology ◽

10.1071/fp14222 ◽

2015 ◽

Vol 42 (3) ◽

pp. 229 ◽

Cited By ~ 18

Author(s):

April H. Hastwell ◽

Peter M. Gresshoff ◽

Brett J. Ferguson

Keyword(s):

Molecular Mechanisms ◽

De Novo ◽

Lotus Japonicus ◽

Peptide Hormones ◽

Negative Feedback Loops ◽

C Terminus ◽

Cle Peptides ◽

Autoregulation Of Nodulation ◽

Cle Peptide ◽

External Stimuli

Legumes form a highly-regulated symbiotic relationship with specific soil bacteria known as rhizobia. This interaction results in the de novo formation of root organs called nodules, in which the rhizobia fix atmospheric di-nitrogen (N2) for the plant. Molecular mechanisms that regulate the nodulation process include the systemic ‘autoregulation of nodulation’ and the local nitrogen-regulation of nodulation pathways. Both pathways are mediated by novel peptide hormones called CLAVATA/ESR-related (CLE) peptides that act to suppress nodulation via negative feedback loops. The mature peptides are 12–13 amino acids in length and are post-translationally modified from the C-terminus of tripartite-domain prepropeptides. Structural redundancy between the prepropeptides exists; however, variations in external stimuli, timing of expression, tissue specificity and presence or absence of key functional domains enables them to act in a specific manner. To date, nodulation-regulating CLE peptides have been identified in Glycine max (L.) Merr., Medicago truncatula Gaertn., Lotus japonicus (Regel) K.Larsen and Phaseolus vulgaris L. One of the L. japonicus peptides, called LjCLE-RS2, has been structurally characterised and found to be an arabinosylated glycopeptide. All of the known nodulation CLE peptides act via an orthologous leucine rich repeat (LRR) receptor kinase. Perception of the peptide results in the production of a novel, unidentified inhibitor signal that acts to suppress further nodulation events. Here, we contrast and compare the various nodulation-suppressing CLE peptides of legumes.

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Nitrate-Induced CLE Peptide Systemically Inhibits Nodulation in Medicago truncatula

Plants ◽

10.3390/plants9111456 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1456

Author(s):

Maria Lebedeva ◽

Mahboobeh Azarakhsh ◽

Yaroslavna Yashenkova ◽

Lyudmila Lutova

Keyword(s):

Medicago Truncatula ◽

Lotus Japonicus ◽

Dependent Manner ◽

Receptor Kinase ◽

Nitrate Treatment ◽

Whole Plant ◽

Cle Peptides ◽

Autoregulation Of Nodulation ◽

Cle Peptide ◽

Plant Level

Legume plants form nitrogen-fixing nodules in symbiosis with soil bacteria rhizobia. The number of symbiotic nodules is controlled at the whole-plant level with autoregulation of nodulation (AON), which includes a shoot-acting CLV1-like receptor kinase and mobile CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides that are produced in the root in response to rhizobia inoculation. In addition to rhizobia-induced CLE peptides, nitrate-induced CLE genes have been identified in Lotus japonicus and Glycine max, which inhibited nodulation when overexpressed. However, nitrate-induced CLE genes that systemically suppress nodulation in AON-dependent manner have not been identified in Medicago truncatula. Here, we found that MtCLE35 expression is activated by both rhizobia inoculation and nitrate treatment in M. truncatula, similarly to L. japonicus CLE genes. Moreover, we found that MtCLE35 systemically suppresses nodulation in AON-dependent manner, suggesting that MtCLE35 may mediate nitrate-induced inhibition of nodulation in M. truncatula.

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Inoculation- and Nitrate-Induced CLE Peptides of Soybean Control NARK-Dependent Nodule Formation

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-10-0207 ◽

2011 ◽

Vol 24 (5) ◽

pp. 606-618 ◽

Cited By ~ 158

Author(s):

Dugald E. Reid ◽

Brett J. Ferguson ◽

Peter M. Gresshoff

Keyword(s):

Amino Acid ◽

Nodule Development ◽

Nodule Formation ◽

Dependent Manner ◽

Transgenic Roots ◽

Nitrate Treatment ◽

Cle Peptides ◽

Autoregulation Of Nodulation ◽

Cle Peptide ◽

Bradyrhizobium Sp

Systemic autoregulation of nodulation in legumes involves a root-derived signal (Q) that is perceived by a CLAVATA1-like leucine-rich repeat receptor kinase (e.g. GmNARK). Perception of Q triggers the production of a shoot-derived inhibitor that prevents further nodule development. We have identified three candidate CLE peptide-encoding genes (GmRIC1, GmRIC2, and GmNIC1) in soybean (Glycine max) that respond to Bradyrhizobium japonicum inoculation or nitrate treatment. Ectopic overexpression of all three CLE peptide genes in transgenic roots inhibited nodulation in a GmNARK-dependent manner. The peptides share a high degree of amino acid similarity in a 12-amino-acid C-terminal domain, deemed to represent the functional ligand of GmNARK. GmRIC1 was expressed early (12 h) in response to Bradyrhizobium-sp.-produced nodulation factor while GmRIC2 was induced later (48 to 72 h) but was more persistent during later nodule development. Neither GmRIC1 nor GmRIC2 were induced by nitrate. In contrast, GmNIC1 was strongly induced by nitrate (2 mM) treatment but not by Bradyrhizobium sp. inoculation and, unlike the other two GmCLE peptides, functioned locally to inhibit nodulation. Grafting demonstrated a requirement for root GmNARK activity for nitrate regulation of nodulation whereas Bradyrhizobium sp.-induced regulation was contingent on GmNARK function in the shoot.

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Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Nucleic Acids Research ◽

10.1093/nar/gkab185 ◽

2021 ◽

Vol 49 (7) ◽

pp. 3856-3875

Author(s):

Marina Kulik ◽

Melissa Bothe ◽

Gözde Kibar ◽

Alisa Fuchs ◽

Stefanie Schöne ◽

...

Keyword(s):

Gene Regulation ◽

Transcription Factor ◽

Dna Binding ◽

Receptor Binding ◽

Binding Sites ◽

Specific Gene ◽

Functional Diversification ◽

Enhancer Activity ◽

Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

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Genome-wide discovery of G-quadruplexes in barley

Scientific Reports ◽

10.1038/s41598-021-86838-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

H. Busra Cagirici ◽

Hikmet Budak ◽

Taner Z. Sen

Keyword(s):

Transcription Initiation ◽

Large Window ◽

First Intron ◽

Domain Sequence ◽

Genome Wide ◽

Square Planar ◽

Peak Points ◽

Molecular Functions ◽

Nucleic Acid Structures ◽

Provided Examples

AbstractG-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

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Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Mobile DNA ◽

10.1186/s13100-019-0186-z ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Pavel Jedlicka ◽

Matej Lexa ◽

Ivan Vanat ◽

Roman Hobza ◽

Eduard Kejnovsky

Keyword(s):

Secondary Structure ◽

In Silico ◽

Negative Impact ◽

Nucleosome Occupancy ◽

Ltr Retrotransposons ◽

Sequence Composition ◽

Plant Genomes ◽

Weak Preference ◽

In Silico Study ◽

Impact On Family

Abstract Background Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements. Results We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons. Conclusions We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.

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Sedimentology, petrography, and reservoir quality of the Zarga and Ghazal formations in the Keyi oilfield, Muglad Basin, Sudan

Scientific Reports ◽

10.1038/s41598-020-80831-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yousif M. Makeen ◽

Xuanlong Shan ◽

Habeeb A. Ayinla ◽

Ekundayo Joseph Adepehin ◽

Ndip Edwin Ayuk ◽

...

Keyword(s):

Thin Section ◽

Sedimentary Facies ◽

Depositional Environments ◽

Coarse Grained ◽

Reservoir Quality ◽

Research Attention ◽

Sequence Composition ◽

Exploration And Production ◽

Authigenic Mineral ◽

Thin Section Analysis

AbstractThe Zarga and Ghazal formations constitute important reservoirs across the Muglad Basin, Sudan. Nevertheless, the sedimentology and diagenesis of these reservoir intervals have hitherto received insignificant research attention. Detailed understanding of sedimentary facies and diagenesis could enhance geological and geophysical data for better exploration and production and minimize risks. In this study, subsurface reservoir cores representing the Zarga formation (1114.70–1118.50 m and 1118.50–1125.30 m), and the Ghazal formation (91,403.30–1406.83 m) were subjected to sedimentological (lithofacies and grain size), petrographic/mineralogic (thin section, XRD, SEM), and petrophysical (porosity and permeability) analyses to describe their reservoir quality, provenance, and depositional environments. Eight (8) different lithofacies, texturally characterized as moderately to well-sorted, and medium to coarse-grained, sub-feldspathic to feldspathic arenite were distinguished in the cored intervals. Mono-crystalline quartz (19.3–26.2%) predominated over polycrystalline quartz (2.6–13.8%), feldspar (6.6–10.3%), and mica (1.4–7.6%) being the most prominent constituent of the reservoir rocks. Provenance plot indicated the sediments were from a transitional continental provenance setting. The overall vertical sequence, composition, and internal sedimentary structures of the lithofacies suggest a fluvial-to-deltaic depositional environment for the Ghazal formation, while the Zarga formation indicated a dominant deltaic setting. Kaolinite occurs mainly as authigenic mineral, while carbonates quantitatively fluctuate with an insignificant amount of quartz overgrowths in most of the analyzed cores. Integration of XRD, SEM, and thin section analysis highlights that kaolinite, chlorite, illite, and smectite are present as authigenic minerals. Pore-destroying diagenetic processes (e.g. precipitation, cementation, and compaction etc.) generally prevailed over pore-enhancing processes (e.g. dissolution). Point-counted datasets indicate a better reservoir quality for the Ghazal formation (ɸ = 27.7% to 30.7%; K = 9.65 mD to 1196.71 mD) than the Zarga formation (17.9% to 24.5%; K = 1051.09 mD to 1090.45 mD).

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