
Hasna BoubakriMicrobial Ecology Lab - University of Lyon 1 · UMR CNRS 5557
Hasna Boubakri
Assistant professor
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41
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Publications (41)
Alnus glutinosa, able to establish symbiosis with mutualistic bacteria of the genus Frankia, is one of the main species in European riparian environments, where it performs numerous biological and socio-economic functions. However, riparian ecosystems face a growing threat from Phytophthora alni, a highly aggressive waterborne pathogen causing seve...
Background
Rhizosphere bacterial community and endophytes are now known to influence plant health and response to environmental stress. Very few studies have reported the diversity of endophytic bacterial communities of Vanilla planifolia and their potential roles in promoting plant growth or contributing to aromatic quality.
Results
In this study...
Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leadi...
Plant root nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by conv...
In this study, 58 endophytic bacterial strains were isolated from pods of two hybrid vanilla plants from Madagascar, Manitra ampotony and Tsy taitra. They were genetically characterized and divided into four distinct phylotypes. Three were associated to genus Bacillus species, and the fourth to the genus Curtobacterium. A selection of twelve strain...
Plant root nodule symbiosis (RNS) with mutualistic nitrogen fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen Fixing Nodulation Clade (NFNC), and is best understood in the legume family. It is widely accepted that nodulation originated through the assembly of modules recruited from existing functions, such as mycorrhizal...
Few studies have been conducted on endophytic bacteria of vanilla. In this study, 58 bacterial strains were isolated from two hybrid vanilla plants from Madagascar, Manitra ampotony and Tsy taitra. They were genetically characterised and divided into four distinct phylotypes. A selection of twelve strains corresponding to the identified genetic div...
The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for “Alnus-infective strains” (i.e., Frankia strains belonging to Cluster Ia). Several genes were specifically found in these s...
Many reviews report induction of defence genes similar with pathogenesis in legume-rhizobia and mycorrhizal symbioses, suggesting it could be a convergent point in plant-microorganism symbiotic systems. However, research in actinorhizal symbiosis versus pathogenesis is still in early stages and much remains to be learned to confirm this hypothesis....
Background
Cadmium (Cd²⁺) is one of the highly toxic heavy metals and is considered as a carcinogenic agent. Our aim was to confirm Frankia alni ACN14a ability to resist Cd²⁺ and determine the genes involved in the resistance.
Results
Up to 10 and 22 times in Cd²⁺ accumulation were detected in F. alni ACN14a and Frankia casuarinae CcI3 hyphae when...
The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were signific...
In the present study, an analysis of antimicrobial activity; and an assessment of genomic biocontrol attributes of the recently described radioresistant strain Kocuria rhizophila PT10 were conducted. PT10, a Gram-positive and yellow pigmented actinobacterial strain, was isolated from the roots of xerophyte Panicum turgidum collected from Ksar Ghila...
Carbon Catabolite Repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes to utilize sec...
The response of Alnus glutinosa to Frankia alni is complex with several sequential physiological modifications that include calcium spiking, root hair deformation, penetration, induction of primordium, formation and growth of nodule. A transcriptomic study of seedlings in hydroponics after early contact (2.5 days) with Frankia alni , either with a...
Symbiosis established between actinorhizal plants and Frankia spp., which are nitrogen-fixing actinobacteria, promotes nodule organogenesis, the site of metabolic exchange. The present study aimed to identify amino acid markers involved in Frankia-Alnus interactions by comparing nodules and associated roots from field and greenhouse samples. Our re...
Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with s...
The purpose of this study was to explore the microbial potential of a semi-arid sandy soil from south-central Algeria in order to isolate new chitinolytic actinobacteria. This soil is subjected to high temperatures (up to 43 °C) and has low nutrient content. Strains were isolated by plating soil suspensions on Bennett and Colloidal Chitin (CCM) med...
The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p < 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) ≥ 2), as well as significant downregulation of 48...
A unique case of microbial symbiont capable of dormancy within its living host cells has been reported in actinorhizal symbioses: some Frankia strains, named Sp+, are able to sporulate inside plant cells, contrarily to Sp- strains. The presence of metabolically slowed down bacterial structures in host cells alters our understanding of symbiosis bas...
Trophic exchanges constitute the bases of the symbiosis between the nitrogen-fixing actinomycete Frankia and its host plant Alnus, but the identity of the compounds exchanged is still poorly known. In the current work, previously published transcriptomic studies of Alnus nodules and of symbiotic Frankia were reexamined for TCA cycle related genes....
Alnus glutinosa has been shown previously to synthesize, in response to nodulation by Frankia sp. ACN14a, an array of peptides called Alnus symbiotic up-regulated peptides (ASUP). In a previous study one peptide (Ag5) was shown to bind to Frankia nitrogen-fixing vesicles and to modify their porosity. Here we analyse 4 other ASUPs, alongside Ag5, to...
Importance:
Streptomyces spp. are filamentous and sporulating actinobacteria, remarkable for their morphological and metabolic differentiation. They produce numerous bioactive compounds, including antifungal, antibiotic and antitumor compounds. There is therefore considerable interest in understanding the mechanisms by which Streptomyces regulate...
Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are suppose...
Quantification of fork breakage.
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Control strains do not produce linear DNA when shifted to rich medium. For all experiments shown in Figure 3, Figure 4, Figure 5, Figure 6, plugs of a control strain expected to show no fork breakage (a non-inverted recB or recA recD mutant, a InvA or InvBE RecBC+ mutant) were prepared in parallel with plugs of Inv recBC or Inv recA recD mutants. E...
Inactivation of the mfd gene does not affect the viability of Inv mutants.
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Strains and plasmids.
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Supplementary references.
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Replication fork arrest is a recognized source of genetic instability, and transcription is one of the most prominent causes of replication impediment. We analyze here the requirement for recombination proteins in Escherichia coli when replication-transcription head-on collisions are induced at a specific site by the inversion of a highly expressed...
Supplementary Information
Review Process File
How living cells deal with head-on collisions of the replication and transcription complexes has been debated for a long time. Even in the widely studied model bacteria Escherichia coli, the enzymes that take care of such collisions are still unknown. We report here that in vivo, the DinG, Rep and UvrD helicases are essential for efficient replicat...
Recombination proteins play crucial roles in the rescue of inactivated replication forks in Escherichia coli. The enzymes that catalyze the repair of DNA double-strand breaks by a classical strand-exchange reaction (RecBCD, RecA) act in two well-characterized fork repair pathways. They repair the DNA double-strand end made when a replication fork r...
We describe a metagenomic DNA shuffling process by combining protein engineering process mutation generator and the high potential diversity of metagenomic DNA derived from the environment. Numerous previous shuffling processes attempted to recombine more or less related parental sequences. At the same time, metagenomic approaches unveiled a huge d...
The lin genes encode the gamma-hexachlorocyclohexane (gamma-HCH or lindane) catabolic pathway in lindane-degrading strains. The location and stability of these genes have been explored in the lindane-degrading Sphingobium francense strain Sp+, and in two non-lindane-degrading mutants (Sp1- and Sp2-). The lin genes, linA, linB, linE and linX were lo...