Biology subjects

Kulikova, O.

Publications and source records attributed to Kulikova, O..

8 recordsLinked to original sources

bioRxiv2026

Nod factor signaling controlled genes in Medicago truncatula nodules

O_LILegume nodule formation is induced by rhizobia secreted Nod factors (NFs). It has been shown that NF receptors also accumulate in the apex of Medicago truncatula nodules. However, the NF signaling induced transcriptional changes in there have never been studied. C_LIO_LIHere, we studied this by using NF signaling mutant TE7, a weak allele of IPD3, blocked in rhizobial release. Nodule apices were isolated with laser microdissection and used for transcriptional analysis. C_LIO_LIWe identified 1655 NF signaling controlled genes in nodule apex. By comparing this with the transcriptome data from VAMP721d&e RNAi nodule apices, we identified a subset of 445 genes whose expression depends on NF signaling and rhizobial release. Further, we compared the set of genes controlled by NF signaling in nodule apices with that controlled in root epidermis, and these showed only a small overlap. NIN is induced by NF signaling both in the root epidermis and in the nodule. By overexpression of NIN in TE7 and knock down of NIN in wildtype nodules we showed that NF signaling controlled rhizobial release depends on NIN. C_LIO_LINF signaling controls a distinct set of genes in nodules, the function of which depends at least in part on NIN. C_LI

Developmental Biology↗

bioRxiv2026

Spatiotemporal dynamics of ethylene biosynthesis shape infection and nodule initiation in Medicago truncatula

Ethylene is a well-established negative regulator of nodulation, yet how ethylene biosynthesis and perception are spatially coordinated during early symbiotic signalling remains unresolved. Here, we investigate the dynamics of ethylene responses in Medicago truncatula using transcriptomics, promoter-reporter analyses, loss-of-function approaches and a synthetic reporter. We show that the activity of the ethylene-responsive EBSn reporter shifts from inner root tissues under non-symbiotic conditions to the outer cortex and epidermis following rhizobial inoculation, revealing a spatial reprogramming of ethylene signalling. Among the eight Medicago 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE (ACS) genes, upon rhizobia application MtACS3 is induced in outer root cell layers, while MtACS10 is repressed in the inner cortex and pericycle, mirroring the shift in ethylene perception. Functional analysis demonstrates that MtACS10 restricts nodule initiation, whereas MtACS3 modulates infection thread number, prevents nodule clustering, and contributes to radial positioning of nodule primordia. Rhizobial induced ectopic ACS expression in the root interior counteracts MtACS10 repression and blocks nodulation, highlighting the requirement for spatially confined downregulation of ethylene biosynthesis. Together, these findings establish a framework in which localized shift in ethylene biosynthesis, mediated by distinct Medicago ACS genes, balances infection and organogenesis while co-defining the spatial limits of the root susceptible zone.

plant biology↗

bioRxiv2025

A PLETHORA transcription factor shapes cucumber shoot architecture

O_LIPLETHORA transcription factors (PLTs) are master regulators of plant development. Loss of shoot meristematic PLTs leads to reduced phyllotactic regularity and robustness in Arabidopsis and increased inflorescence branching in tomato. Whether these factors have similar functions in other species is not known. C_LIO_LITo address this knowledge gap, we integrated phylogenetic, transcriptomic, and genome-wide in vitro binding strategies with quantitative shoot architecture phenotyping of a panel of cucumber TILLING mutants of each CsPLT homolog. C_LIO_LIWe determined that CsPLT3/7 and CsPLT are expressed in complementary domains in the cucumber shoot apex. DAP-seq data indicated that both transcription factors recognised an ANT-like consensus motif and bound to SAM organising genes. We identified strong phenotypic defects in multiple Csplt3/7 mutants. In mature seeds, Csplt3/7 mutants formed a flat apex instead of a shoot apical meristem, from which secondary meristems emerged during subsequent seedling development. Mature Csplt3/7 shoots exhibited defects in internode length regularity, stem architecture, flower morphology, and axillary organ initiation. Moreover, phyllotactic patterns were slightly shifted from a spiral towards a distichous orientation. C_LIO_LIWe present one of the first pieces of evidence that the PLT3/7 clade fulfils both conserved and diversified roles in shoot development across taxonomic family boundaries. C_LI

plant biology↗

bioRxiv2025

Evolutionary predisposition of NIN to function in nitrogen-fixing nodules

Nitrogen-fixing nodule symbiosis is an ecologically and economically important trait in legumes and some related species. A critical step in the evolution of nodulation is the recruitment of NODULE INCEPTION (NIN); a homolog of the nitrate-sensing NIN-LIKE PROTEIN (NLP) transcription factors. However, whether adaptations have occurred in the NIN protein upon its recruitment in symbiosis remains elusive. Here we show that non-symbiotic NIN orthologs can function in intracellular infection and even nodule initiation, demonstrating that these properties of NIN predate the evolution of nodulation. Concurrent with the evolution of nodulation, symbiotic NIN proteins were optimized for their role in symbiosis by acquiring nitrate independent functionality, including constitutive nuclear localization. A single amino acid substitution in Arabidopsis AtNLP2 enhances its nuclear localization under low nitrate conditions, making it functionally comparable to a symbiotic NIN. These findings highlight that NIN was predisposed to function in nodulation at the time of its recruitment into nitrogen-fixing symbiosis. Our study provides novel insight in how and why non-symbiotic NIN orthologues could be recruited to function in nitrogen-fixing root nodule symbiosis.

plant biology↗

bioRxiv2023

Nodule organogenesis in Medicago truncatula requires local stage-specific auxin biosynthesis and transport

The importance of auxin in plant organ development including root nodule formation is well established. Using auxin reporter constructs the spatiotemporal auxin distribution pattern during nodule development has previously been illustrated. However, our understanding of how this pattern is built-up and maintained still remains elusive. To this end, we studied how the auxin gradient visualized by DR5 expression patterns at different stages of nodule development in Medicago truncatula (Medicago), is correlated with the spatiotemporal expression patterns of known auxin biosynthesis and auxin transport genes. In addition, we record the MtPIN10-GFP expression pattern and polar positioning on the cell plasma membranes during nodule primordium development to investigate the auxin flux. RNA interference and the application of auxin synthesis blockers were used to demonstrate the relevance of biosynthesis and transport at the initial stages of the nodulation process. Our results show that upon rhizobium inoculation, preceding the first mitotic activity, a specific set of MtYUCs and MtPINs as well as MtLAX2 are expressed in the pericycle contributing to the creation of an auxin maximum. Overall, we demonstrate that dynamic spatiotemporal expression of both, MtYUCs and MtPINs, result in specific auxin outputs in subsequent stages of nodule primordia and nodule meristem formation.

plant biology↗

bioRxiv2023

Conserving bird populations in the Anthropocene: the significance of non-breeding movements

Advances in tracking technologies have revealed the diverse migration patterns of birds, which are critical for range mapping and population estimation. Population trends are usually estimated in breeding ranges where birds remain stationary, but for species that breed in remote areas like the Arctic, these trends are often assessed in over-wintering ranges. Evaluating population trends during the wintering season is challenging due to the extensive movements of birds in these ranges, which require a deep understanding of the movement dynamics. However, these movements remain understudied, particularly in the mid-latitudes, where many Arctic breeders overwinter, increasing uncertainty in their ranges and numbers. Here, we show that the Arctic breeding raptor Rough-legged buzzard, which overwinters in the mid-latitudes, has a specific wintering strategy. After migrating ca 1,500 km from the Arctic to mid-latitudes, the birds continue to move throughout the entire over-wintering period, covering an additional 1,000 km southwestward and then back northeastward as the snowline advances. This ongoing movement makes their wintering range dynamic over the course of the season. In essence, this movement represents an extension of the quick migration process, albeit at a slower pace, and we have termed this migration pattern foxtrot migration, drawing an analogy to the alternating fast and slow movements of the foxtrot dance. These results highlight the potential errors in range mapping from single mid-winter surveys and emphasize the importance of this migration pattern in assessing the conservation status of bird species. Understanding this migration pattern could help to correctly estimate bird populations in over-wintering ranges, which is especially important for species that nest in hard-to-reach regions such as the Arctic.

ecology↗

bioRxiv2020

Plant-specific histone deacetylases are essential for early as well as late stages of Medicago nodule development

Legume and rhizobium can establish a nitrogen-fixing nodule symbiosis. Previous studies have shown that several transcription factors that play a role in (lateral) root development are also involved in nodule development. Chromatin remodelling factors, like transcription factors, are key players in regulating gene expression. However, it has not been studied whether chromatin remodelling genes that are essential for root development get involved in nodule development. Here we studied the role of Medicago histone deacetylases (MtHDTs) in nodule development. Their Arabidopsis orthologs have been shown to play a role in root development. The expression of MtHDTs is induced in nodule primordia and is maintained in nodule meristem and infection zone. Conditional knock-down of their expression in a nodule-specific way by RNAi blocks nodule primordium development. A few nodules still can be formed but their nodule meristems are smaller and rhizobial colonization of the cells derived from the meristem is markedly reduced. Although the HDTs are expressed during nodule and root development, transcriptome analyses indicate that HDTs control the development of these organs in a different manner. During nodule development the MtHDTs positively regulate 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 (MtHMGR1). The decreased expression of MtHMGR1 is sufficient to explain the block of primordium formation. ONE SENTENCE SUMMARYPlant-specific histone deacetylases regulate the expression of 3-hydroxy-3-methylglutaryl-coenzyme A reductases to control root nodule development.

developmental biology↗

bioRxiv2020

Sea-crossing along migratory flyways is limited more strongly by wind than by lack of uplift

Flying over the open sea is energetically costly for terrestrial birds. Despite this, over-water journeys of many birds, sometimes hundreds of kilometers long, are uncovered by bio-logging technology. To understand how these birds afford their flights over the open sea, we investigated the role of atmospheric conditions, specifically wind and uplift, in subsidizing over-water flight at the global scale. We first established that {Delta}T, the temperature difference between sea surface and air, is a meaningful proxy for uplift over water. Using this proxy, we showed that the spatio-temporal patterns of sea-crossing in terrestrial migratory birds is associated with favorable uplift conditions. We then analyzed route selection over the open sea for five facultative soaring species, representing all major migratory flyways. The birds maximized wind support when selecting their sea-crossing routes and selected higher uplift when suitable wind support was available. They also preferred routes with low long-term uncertainty in wind conditions. Our findings suggest that, in addition to wind, uplift may play a key role in the energy seascape for bird migration that in turn determines strategies and associated costs for birds crossing ecological barriers such as the open sea.

animal behavior and cognition↗