Biology subjects

Hanikenne, M.

Publications and source records attributed to Hanikenne, M..

17 recordsLinked to original sources

bioRxiv2026

Zinc and iron homeostatic interactions in a mutant lacking nicotianamine vacuolar storage and citrate xylem loading

Metal homeostasis in plants relies on coordinated uptake, chelation, and transport mechanisms involving, but not limited to, citrate and nicotianamine (NA). In Arabidopsis (Arabidopsis thaliana), disruption of the citrate exporter FRD3 (FERRIC REDUCTASE DEFECTIVE 3) causes constitutive Fe deficiency responses, altered iron (Fe), manganese (Mn) and zinc (Zn) distribution, with Fe accumulation in the root cell wall. This ultimately results in oxidative and biotic stress responses, and impaired root development, phenotypes that are partially alleviated by Zn excess. In this study, we investigated the consequences of impairing both citrate loading into xylem vessels and NA partitioning within cells. The frd3 zif1 double mutant exhibits enhanced sensitivity to Zn excess, severe defects in root system architecture and meristem maintenance, persistent oxidative stress, and compromised reproductive development. These phenotypes correlate with sustained activation of Fe deficiency signaling and marked defects in root-to-shoot metal translocation. Our findings reveal that coordinated citrate export and NA compartmentation form an integrated buffering strategy required to maintain metal homeostasis and partitioning, as well as redox balance and proper development, including root plasticity and seed yield, under fluctuating metal availability.

plant biology↗

bioRxiv2025

Zinc deficiency induces spatially distinct responses in roots and impacts ZIP12-dependent zinc homeostasis in Arabidopsis

How zinc (Zn) deficiency shapes root development remains unclear, with conflicting reports on its effect on primary root growth in Arabidopsis thaliana (Arabidopsis). The impact of Zn shortage on the root apical meristem (RAM) in particular has not been systematically explored. Using an integrative approach combining cell biology, transcriptomics, and ionomics, we dissected how Zn deficiency alters root zonation and function. We showed that Zn deficiency triggers a striking reorganization of the root tip (RT): the RAM size is reduced, yet meristematic activity and local Zn levels are preserved. This is accompanied by promoted cell elongation and differentiation. Transcriptome profiling revealed a distinct Zn deficiency response in the RAM-enriched RT compared to mature root tissues, with ZIP12 emerging as the most strongly induced gene in the RT. Functional analysis of zip12 mutants uncovered major defects in root growth, RAM structure, expression of Zn-responsive genes, and metal partitioning. Our work unveiled a new layer of root developmental plasticity under Zn deficiency and identified ZIP12 as a central player in maintaining Zn homeostasis and root meristem function in Arabidopsis. These findings provide a framework to better understand how plants adapt root growth to fluctuating micronutrient availability.

plant biology↗

bioRxiv2025

The antifungal and other bioactive properties of the volatilome of Streptomyces scabiei

Volatile compounds (VCs) produced by most host-associated bacteria remain largely unexplored despite their potential roles in suppressing microbial competitors and facilitating host colonization. This study investigated the volatilome of Streptomyces scabiei 87-22, the model species for causative agents of common scab in root and tuber crops, under culture conditions that completely inhibited fungal growth, including the phytopathogens Alternaria solani and Gibberella zeae. Bicameral assays confirmed that these inhibitory effects were at least partially mediated by VCs. Using GC x GC TOFMS, 36 VCs were unambiguously identified as products of S. scabiei 87-22 metabolic activity. These included mainly ketones and aromatic compounds (both benzene derivatives and heterocycles), along with smaller contributions from other chemical families including sulfur-containing compounds, nitriles, esters, terpenoids, an amide, and an aldehyde. A literature survey suggests that many of these VCs possess antibacterial, antifungal, anti-oomycete, nematocidal, and insecticidal effects, while the bioactivity of others remains speculative, having been identified only within complex volatile mixtures. Among those with known antifungal properties, dimethyl trisulfide, 2-heptanone, and creosol inhibited the growth of the fungal pathogens tested in this study. In addition, we reveal here that 3-penten-2-one is also a strong inhibitor of fungal growth. Remarkably, despite S. scabiei 87-22 being defined as a pathogen, some of its VCs were associated with plant growth promotion and defense stimulation. Overall, our work highlights the remarkable potential of S. scabiei 87-22 to produce VCs with diverse bioactivities including fungal pathogen inhibition and priming plant resistance. ImportanceThis study reveals that Streptomyces scabiei, the bacterium causing common scab in root and tuber crops, produces a wide variety of volatile chemicals with surprising benefits. These natural compounds can inhibit growth of other harmful microbes, including fungal plant pathogens. Some of these chemicals are already known to fight pests and diseases, while others, like 3-penten-2-one, are newly discovered as potential antifungals. Even more unexpectedly, some of the identified compounds may help plants grow or boost their defenses. Combined with previous work, our findings challenge the idea that S. scabiei is purely harmful and suggests it might, under certain conditions, play a protective role in its environment. This work deepens our understanding of how microbes interact with each other and with plants, and could help shape more sustainable approaches to agriculture.

microbiology↗

bioRxiv2024

Cis-regulatory mutations co-opting circadian clock regulation underlie naturally selected extreme trait in Arabidopsis halleri

HEAVY METAL ATPase 4 (HMA4) is required for the naturally selected traits of zinc/cadmium hyperaccumulation and hypertolerance of in Arabidopsis halleri. Cis-regulatory alterations and tandem triplication of AhHMA4 result in substantially elevated transcript levels compared to the closely related non-tolerant non-hyperaccumulator Arabidopsis thaliana. Here we identify cis-regulatory Metal Hyperaccumulation Elements (MHEs) necessary for AhHMA4 promoter activity, employing sequence comparisons and motif elicitation analyses combined with progressive deletions and site-directed mutagenesis of promoter-reporter constructs. We report that the promoters of all AhHMA4 gene copies share a distal MHE1 (consensus TGTAAC), and a proximal pair of MHE2s identical or highly similar to the Evening Element (AAAATATCT). Evening elements are known binding sites of Arabidopsis CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), a phytochrome-regulated transcription factor in the core circadian clock. We show that the promoter of each AhHMA4 gene copy, but not of AtHMA4, mediates enhanced transcript levels of the reporter and their diel rhythmicity. These functional characteristics are CCA1-dependent and recapitulated by a synthetic reporter construct placing the MHE2 pair into the AtHMA4-promoter sequence context, according to the example of the AhHMA4-1 promoter. Consistent with our observations in transgenic reporter lines, AhHMA4 transcript levels follow a diel rhythm in wild-type A. halleri plants. Different from A. halleri, we identify complex repressive functionalities co-localizing with an upstream lncRNA and an intron in the 5 untranslated region of A. thaliana HMA4. In summary, our work exemplifies how cis-regulatory mutations contributed to the evolution of extreme physiological traits through the co-option of the circadian clock regulatory network.

plant biology↗

bioRxiv2024

The Arabidopsis RS2Z32 and RS2Z33 proteins are dynamic splicing factors whose RNA recognition motif (RRM) domain contributes to protein-protein and protein-RNA interactions

The Arabidopsis splicing factors arginine/serine-rich zinc knuckle-containing proteins 32 and 33 (RS2Z32 and RS2Z33) are plant-specific members of the SR family whose molecular functions received little attention. Here, we characterized both RS2Z32 and RS2Z33 by examining their expression profile at different stages of development and their spatial cellular distribution, as well as the contribution of their domains in the establishment of protein-protein interactions and RNA binding specificity. We report that the RS2Z32 and RS2Z33 promoters are ubiquitously active during vegetative and reproductive growth, and that both RS2Z splicing factors localize in the nucleus (except the nucleolus). We show that the C-terminal arginine/serine-rich (RS) domain, but not the serine/proline-rich (SP) extension, is a determinant of nuclear localization, which likely requires phosphoresidues putatively phosphorylated by kinases of the SRPK family. We demonstrate that their RNA recognition motif (RRM) domain specifically binds pyrimidine-rich RNA motifs via three residues (Y14, Y46, F48), and is also involved in protein-protein interactions with at least three SR proteins, namely SR45, SCL30, and SR34. Finally, we show that mutations in RNA-binding domains (i.e. RRM and zinc knuckles, ZnKs) affect the nucleocytoplasmic dynamics of both RS2Z proteins. Our findings provide molecular evidence for the involvement of plant-specific SR splicing factors into the regulation of the splicing process. HighlightSpecific domains of the Arabidopsis RS2Z splicing factors contribute to their nuclear localization, nucleocytoplasmic dynamics, and ability to contact protein partners and specific pyrimidine-rich RNA motifs.

plant biology↗

bioRxiv2024

Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess

O_LIZinc (Zn) excess negatively impacts primary root growth in Arabidopsis. Yet, the effects of Zn excess on specific growth processes in the root tip remain largely unexplored. C_LIO_LITranscriptomics, ionomics and metabolomics were used to examine the specific impact of Zn excess on the root tip (RT) compared to the remaining root (RR). C_LIO_LIZn excess exposure resulted in shortened root apical meristem and elongation zone, with differentiation initiating closer to the tip of the root. Zn accumulated at a lower concentration in the RT than in RR. This pattern was associated with lower expression of Zn homeostasis and Fe deficiency response genes. C_LIO_LIA distinct distribution of Zn and Fe in RT and RR was highlighted by Laser Ablation ICP-MS analysis. C_LIO_LISpecialized Trp-derived metabolism genes, typically associated with redox and biotic stress responses, were specifically up-regulated in the RT upon Zn excess, among those Phytoalexin Deficient 3 (PAD3) encoding the last enzyme of camalexin synthesis. In roots of wild-type seedlings, camalexin concentration increased by 6-fold upon Zn excess and a pad3 mutant displayed increased Zn sensitivity and an altered ionome. C_LIO_LIOur results indicate that distinct redox and iron homeostasis mechanisms are key elements of the response to Zn excess in the RT. C_LI

plant biology↗

bioRxiv2024

A multi-omics analysis of Arabidopsis thaliana root tips under Cd exposure: A role of HY5 in limiting accumulation

O_LICadmium (Cd) is a major environmental pollutant with high toxicity potential. Even though a reduction of growth, including the primary root, is a clear consequence of Cd exposure, a profound understanding of the impact of Cd on the root apical meristem (RAM) and the elongation/differentiation zone (EDZ) is still lacking. C_LIO_LIIn this study, Arabidopsis thaliana roots were subjected to Cd and divided into root tips (RT) and remaining roots (RR) to separately assess the effect of Cd using transcriptomics, ionomics and metabolomics. C_LIO_LIElemental profiling revealed lower Cd accumulation in RT and differences in mineral contents between RT and RR. Transcriptomic analysis demonstrated distinct gene expression patterns in RT and RR, with Cd having less impact in RT. Functional enrichment analysis revealed genes associated with iron and sulfur homeostasis as well as the response to light in both RR and RT. RT-specific responses to Cd included several genes regulated by the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and notably, the hy5 mutant showed increased Cd sensitivity and accumulation compared to the wild type. C_LIO_LIThis study provides comprehensive insights into the inhibitory effects of Cd on primary root growth, elucidating molecular mechanisms involved, particularly highlighting the role of HY5 in Cd accumulation. C_LI

plant biology↗

bioRxiv2023

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava

Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging. In the present study, we generated BAC libraries of the CMD- susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identified and sequenced BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequenced and assembled the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps revealed discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC guided approach to assess cassava genome assemblies significantly improved the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identified 81 stress resistance proteins present in the CMD2 region, amongst which 31 were previously not reported in publicly available CMD2 sequences.

genomics↗

bioRxiv2023

Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents

Withdrawal StatementThe authors have withdrawn their manuscript owing to the fact that the P. infestans strain received from third parties is not the one referred in the manuscript despite having the certificate from the providing collection. All the experiments and data are correct but not included into a proper research context. A new version of this work will be published in near future. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

microbiology↗

bioRxiv2023

The Arabidopsis SR45 splicing factor bridges the splicing machinery and the exon-exon junction complex

The Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. The sr45-1 loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each of SR45 domains by examining their involvement in: (i) the spatial distribution of SR45, (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components, and (iii) the RNA binding specificity. We report that the endogenous SR45 promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RNA recognition motif (RRM) domain specifically binds purine-rich RNA motifs via three residues (H101, H141, Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues likely phosphorylated by kinases from both CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies. HighlightThe contribution of the Arabidopsis SR45 splicing factor individual domains to its nuclear localization, ability to contact in planta novel protein partners and specifically bind RNA motifs was examined.

plant biology↗

bioRxiv2021

Altered metal distribution in the sr45-1 Arabidopsis mutant causes developmental defects

The plant SR (serine/arginine-rich) splicing factor SR45 plays important roles in several biological processes, such as splicing, DNA methylation, innate immunity, glucose regulation and ABA signaling. A homozygous Arabidopsis sr45-1 null mutant is viable, but exhibits diverse phenotypic alterations, including delayed root development, late flowering, shorter siliques with fewer seeds, narrower leaves and petals, and unusual numbers of floral organs. Here, we report that the sr45-1 mutant presents an unexpected constitutive iron deficiency phenotype characterized by altered metal distribution in the plant. RNA-Sequencing highlighted severe perturbations in metal homeostasis, phenylpropanoid pathway, oxidative stress responses, and reproductive development. Ionomic quantification and histochemical staining revealed strong iron accumulation in the sr45-1 root tissues accompanied by an iron starvation in aerial parts. We showed that some sr45-1 developmental abnormalities can be complemented by exogenous iron supply. Our findings provide new insight into the molecular mechanisms governing the phenotypes of the sr45-1 mutant. One sentence summaryThe sr45-1 mutation affects Fe homeostasis, which results in reproductive defects

plant biology↗

bioRxiv2020

Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67Zn isotope revealed whole plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1893 zinc-responsive genes. Multiple ZIP transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.

plant biology↗

bioRxiv2019

Resolution of the proteome, transcript and ionome dynamics upon Zn re-supply in Zn-deficient Arabidopsis

O_LIRegulation of plant Zn acquisition is poorly understood, while Zn deficiency affects over 2 billion people worldwide. We therefore dissected the dynamic response to changes in Zn supply in Arabidopsis. C_LIO_LIHydroponically-grown Zn starved plants were re-supplied with Zn. Subsequent time-resolved sampling strategy allowed concomitant quantification of the dynamics of Zn uptake, microsomal and soluble proteins, and specific transcripts, in space (roots and shoots) and time. C_LIO_LIZn accumulates in roots within 10min, but 8h are needed before shoot Zn increases. By 8h, root Zn concentration was ~60% of non-starved plants. Overexpressed root Zn transporters further peaked in 10-30min post re-supply, before reaching a minimum in 120min and 200 ppm Zn. Zn-responding signaling/regulatory molecules include receptor and MAP kinases, calcium signaling proteins, phosphoinositides, G-proteins, COP9 signalosome members, as well as multiple transcription factors. C_LIO_LIZn acquisition is a highly controlled dynamic process. Our study identifies novel players in Zn homeostasis and points to cross-talk with other nutrients. It paves the way for directed investigation of so far omitted candidates which dynamically respond to sudden changes in Zn supply but are expressed at similar levels at steady-state Zn deficiency and sufficiency. C_LI

plant biology↗

bioRxiv2018

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Transposable elements (TEs) have initially been viewed as pure genomic parasites but are now recognized as central genome architects and powerful agents of rapid adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either recent or old insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. TE fragments that have been maintained in both species, i.e. those that are orthologous, tend to be located on average closer to genes than those that are retained in one species only. Moreover, compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing TE insertions when they are close to genes. Overall, our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

evolutionary biology↗

bioRxiv2018

Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

Cyanobacteria form one of the most diversified phylum of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we deploy a metagenomic pipeline that enables the easy recovery of high-quality genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.\n\nImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.

genomics↗

bioRxiv2017

Assessment Of The Potential Role Of Streptomyces In Cave Moonmilk Formation

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real bacterial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic versus abiotic) involved. In this work we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originating Streptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3 deposition. The metabolic activities involved in CaCO3 transformation were furthermore assessed in vitro among the collection of moonmilk Streptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally, in silico search for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2 allowed to identify genetic predispositions for carbonate precipitation in Streptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.

microbiology↗

bioRxiv2016

PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.

bioinformatics↗