scholarly journals The Frankia alni Symbiotic Transcriptome

2010 ◽  
Vol 23 (5) ◽  
pp. 593-607 ◽  
Author(s):  
Nicole Alloisio ◽  
Clothilde Queiroux ◽  
Pascale Fournier ◽  
Petar Pujic ◽  
Philippe Normand ◽  
...  
Keyword(s):  
Ammonium Assimilation ◽  
Alnus Glutinosa ◽  
Nodule Bacteria ◽  
Free Living ◽  
Iron Cluster ◽  
Peptidoglycan Biosynthesis ◽  
Expression Of Genes ◽  
Frankia Alni ◽  
Plant Families ◽  
Export Protein

The actinobacteria Frankia spp. are able to induce the formation of nodules on the roots of a large spectrum of actinorhizal plants, where they convert dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living Frankia alni cells and on Alnus glutinosa nodule bacteria, using whole-genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia spp. genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to nitrogen fixation were highly induced, nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster), and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified, suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signaling processes, protein drug export, protein secretion, lipopolysaccharide, and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We also showed that this Frankia symbiotic transcriptome was highly similar among phylogenetically distant plant families Betulaceae and Myricaceae. Finally, comparison with rhizobia transcriptome suggested that F. alni is metabolically more active in symbiosis than rhizobia.

scholarly journals Early transcriptomic response of Alnus glutinosa to Frankia alni symbiont, an upregulated nsLTP (non-specific Lipid Transfer Protein) is implicated in early and late stages of symbiosis

2021 ◽  
Author(s):  
Melanie Gasser ◽  
Nicole Alloisio ◽  
Pascale Fournier ◽  
Severine Balmand ◽  
Ons Kharrat ◽  
...  
Keyword(s):  
Root Hair ◽  
Lipid Transfer Protein ◽  
Alnus Glutinosa ◽  
Lipid Transfer ◽  
Transcriptomic Response ◽  
Transfer Protein ◽  
Root Hair Deformation ◽  
Frankia Alni ◽  
Late Stages ◽  
Specific Lipid

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 culture supernatant or with living cells separated from the roots by a dialysis membrane, permitted to identify plant genes which expression level was modified upon early contact with Frankia. Forty-two genes were significantly up-regulated in both experiments, most of them encoding biological processes such as oxidative stress or response to stimuli. Among them, the most upregulated gene was a non-specific lipid transfer protein encoding gene with a fold change of 141. This nsLTP was found to increase Frankia nitrogen fixation at sub-lethal concentration. Interestingly, it was immunolocalized to a region of the deformed root hair at an early infection stage and later in nodules, it was localized around bacterial vesicles suggesting a role in early and late stages of symbiosis.

scholarly journals The Transcriptome of Bathymodiolus azoricus Gill Reveals Expression of Genes from Endosymbionts and Free-Living Deep-Sea Bacteria

Marine Drugs ◽  
2012 ◽  
Vol 10 (12) ◽  
pp. 1765-1783 ◽  
Author(s):  
Conceição Egas ◽  
Miguel Pinheiro ◽  
Paula Gomes ◽  
Cristina Barroso ◽  
Raul Bettencourt
Keyword(s):  
Deep Sea ◽  
Free Living ◽  
Expression Of Genes ◽  
Deep Sea Bacteria

Differentially expressed genes reveal adaptations between free-living and symbiotic niches of Vibrio fischeri in a fully established mutualism

2006 ◽  
Vol 52 (12) ◽  
pp. 1218-1227 ◽  
Author(s):  
B W Jones ◽  
M K Nishiguchi
Keyword(s):  
Gene Expression ◽  
Host Specificity ◽  
Differentially Expressed Genes ◽  
Vibrio Fischeri ◽  
Differentially Expressed ◽  
Light Organ ◽  
Free Living ◽  
Expression Of Genes ◽  
Unique System ◽  
Insight Into

A major force driving in the innovation of mutualistic symbioses is the number of adaptations that both organisms must acquire to provide overall increased fitness for a successful partnership. Many of these symbioses are relatively dependent on the ability of the symbiont to locate a host (specificity), as well as provide some novel capability upon colonization. The mutualism between sepiolid squids and members of the Vibrionaceae is a unique system in which development of the symbiotic partnership has been studied in detail, but much remains unknown about the genetics of symbiont colonization and persistence within the host. Using a method that captures exclusively expressed transcripts in either free-living or host-associated strains of Vibrio fischeri, we identified and verified expression of genes differentially expressed in both states from two symbiotic strains of V. fischeri. These genes provide a glimpse into the microhabitat V. fischeri encounters in both free-living seawater and symbiotic host light organ-associated habitats, providing insight into the elements necessary for local adaptation and the evolution of host specificity in this unique mutualism.Key words: Vibrionaceae, gene expression, Sepiolidae, Euprymna, SCOTS.

scholarly journals Transcriptome Analysis of Durusdinium Associated with the Transition from Free-Living to Symbiotic

2021 ◽  
Vol 9 (8) ◽  
pp. 1560
Author(s):  
Ikuko Yuyama ◽  
Naoto Ugawa ◽  
Tetsuo Hashimoto
Keyword(s):  
High Stress ◽  
Free Living ◽  
False Discovery Rates ◽  
False Discovery ◽  
Expression Of Genes ◽  
Photosynthesis Genes ◽  
Student’S T ◽  
Shock Proteins ◽  
Related Proteins ◽  
Student’S T Test

To detect the change during coral–dinoflagellate endosymbiosis establishment, we compared transcriptome data derived from free-living and symbiotic Durusdinium, a coral symbiont genus. We detected differentially expressed genes (DEGs) using two statistical methods (edgeR using raw read data and the Student’s t-test using bootstrap resampling read data) and detected 1214 DEGs between the symbiotic and free-living states, which we subjected to gene ontology (GO) analysis. Based on the representative GO terms and 50 DEGs with low false discovery rates, changes in Durusdinium during endosymbiosis were predicted. The expression of genes related to heat-shock proteins and microtubule-related proteins tended to decrease, and those of photosynthesis genes tended to increase. In addition, a phylogenetic analysis of dapdiamide A (antibiotics) synthase, which was upregulated among the 50 DEGs, confirmed that two genera in the Symbiodiniaceae family, Durusdinium and Symbiodinium, retain dapdiamide A synthase. This antibiotic synthase-related gene may contribute to the high stress tolerance documented in Durusdinium species, and its increased expression during endosymbiosis suggests increased antibacterial activity within the symbiotic complex.

scholarly journals Point Mutations in a Peptidoglycan Biosynthesis Gene Cause Competence Induction in Haemophilus influenzae

2000 ◽  
Vol 182 (12) ◽  
pp. 3323-3330 ◽  
Author(s):  
Caixia Ma ◽  
Rosemary J. Redfield
Keyword(s):  
Haemophilus Influenzae ◽  
Signal Sequence ◽  
Point Mutations ◽  
Cell Permeability ◽  
Dna Uptake ◽  
Peptidoglycan Biosynthesis ◽  
Peptidoglycan Synthesis ◽  
Expression Of Genes ◽  
Conserved Residue ◽  
Competence Induction

ABSTRACT We have identified three new Haemophilus influenzaemutations causing cells to exhibit extreme hypercompetence at all stages of growth. The mutations are in murE, which encodes the meso-diaminopimelate-adding enzyme of peptidoglycan synthesis. All are point mutations causing nonconservative amino acid substitutions, two at a poorly conserved residue (G435→R and G435→W) and the third at a highly conserved leucine (L361→S). The mutant strains have very similar phenotypes and do not exhibit any defects in cell growth, permeability, or sensitivity to peptidoglycan antibiotics. Cells retain the normal specificity of DNA uptake for the H. influenzae uptake signal sequence. The mutations do not bypass genes known to be needed for competence induction but do dramatically increase expression of genes required for the normal pathway of DNA uptake. We conclude that the mutations do not act by increasing cell permeability but by causing induction of the normal competence pathway via a previously unsuspected signal.

scholarly journals Distinct Patterns of Symbiosis-Related Gene Expression in Actinorhizal Nodules from Different Plant Families

2003 ◽  
Vol 16 (9) ◽  
pp. 796-807 ◽  
Author(s):  
Katharina Pawlowski ◽  
Susan Swensen ◽  
Changhui Guan ◽  
Az-Eddine Hadri ◽  
Alison M. Berry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Alnus Glutinosa ◽  
Actinorhizal Plants ◽  
Gene Expression Patterns ◽  
Homologous Genes ◽  
Molecular Phylogenetic ◽  
Plant Families

Phylogenetic analyses suggest that, among the members of the Eurosid I clade, nitrogen-fixing root nodule symbioses developed multiple times independently, four times with rhizobia and four times with the genus Frankia. In order to understand the degree of similarity between symbiotic systems of different phylogenetic subgroups, gene expression patterns were analyzed in root nodules of Datisca glomerata and compared with those in nodules of another actinorhizal plant, Alnus glutinosa, and with the expression patterns of homologous genes in legumes. In parallel, the phylogeny of actinorhizal plants was examined more closely. The results suggest that, although relationships between major groups are difficult to resolve using molecular phylogenetic analysis, the comparison of gene expression patterns can be used to inform evolutionary relationships. In this case, stronger similarities were found between legumes and intracellularly infected actinorhizal plants (Alnus) than between actinorhizal plants of two different phylogenetic subgroups (Alnus/Datisca).

scholarly journals Artificial activation of nif gene expression in nodule bacteria Ex Planta

2019 ◽  
Vol 17 (2) ◽  
pp. 35-42
Author(s):  
Andrey K. Baymiev ◽  
Roman S. Gumenko ◽  
Anastasiya A. Vladimirova ◽  
Ekaterina S. Akimova ◽  
Zilya R. Vershinina ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Regulatory Protein ◽  
Inducible Promoter ◽  
Nitrogen Fixing ◽  
Nodule Bacteria ◽  
Free Living ◽  
Living State ◽  
Artificial Activation ◽  
Nifa Gene

Background. Rhizobia are the most effective nitrogen-fixing organisms that can fix nitrogen only in symbiosis with leguminous plants. The general transcriptional activator of nitrogen fixation genes in diazotrophic bacteria is NifA. In this work, the possibility of modifying the regulation of nitrogen fixation in the nodule bacteria Mesorhizobium, Ensifer and Rhizobium was studied by introducing an additional copy of the nifA gene into the bacterial genomes during the regulation of induced bacterial promoters. Materials and methods. A series of expression genetic constructs with NifA genes of nodule bacteria strains under the control of an inducible promoter Pm were created. The resulting constructs were transformed into strains of nodule bacteria. The obtained recombinant strains were investigated for the appearance of their nitrogen-fixing activity in the free-living state. Results. It was shown that the expression of nifA in recombinant cells of all three genera of bacteria leads to the appearance of insignificant nitrogenase activity. At the same time, the level of nitrogenase activity does not have a correlation with the level of expression of the introduced nifA gene, which, most likely, is a consequence of the multilevel regulation of nitrogen fixation. Conclusion. The possibility of artificial activation of nitrogenase activity in nodule bacteria in the free-living state by introducing the NifA regulatory protein gene into bacteria was shown.

Nutritional constraints on root nodule bacteria affecting symbiotic nitrogen fixation: a review

2001 ◽  
Vol 41 (3) ◽  
pp. 417 ◽  
Author(s):  
G. W. O'Hara
Keyword(s):  
Nitrogen Fixation ◽  
Root Nodule ◽  
Nutrient Deficiency ◽  
Nodule Development ◽  
Nutrient Deficiencies ◽  
Nodule Bacteria ◽  
Free Living ◽  
Root Nodule Bacteria ◽  
Molecular Approaches ◽  
Calcium Iron

Root nodule bacteria require access to adequate concentrations of mineral nutrients for metabolic processes to enable their survival and growth as free-living soil saprophytes, and in their symbiotic relationship with legumes. Essential nutrients, with a direct requirement in metabolism of rhizobia are carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, potassium, calcium, magnesium, iron, manganese, copper, zinc, molybdenum, nickel, cobalt and selenium. Boron does not seem to be required by rhizobia, but is essential for the establishment of effective legume symbioses. Nutrient constraints can affect both free-living and symbiotic forms of root nodule bacteria, but whether they do is a function of a complex series of events and interactions. Important physiological characteristics of rhizobia involved in, or affected by, their mineral nutrition include nutrient uptake, growth rate, gene regulation, nutrient storage, survival, genetic exchange and the viable non-culturable state. There is considerable variation between genera, species and strains of rhizobia in their response to nutrient deficiency. The effects of nutrient deficiencies on free-living rhizobia in the soil are poorly understood. Competition between strains of rhizobia for limiting phosphorus and iron in the rhizosphere may affect their ability to nodulate legumes. Processes in the development of some legume symbioses specifically require calcium, cobalt, copper, iron, potassium, molybdenum, nickel, phosphorus, selenium, zinc and boron. Limitations of phosphorus, calcium, iron and molybdenum in particular, can reduce legume productivity by affecting nodule development and function. The effects of nutrient deficiencies on rhizobia–legume signalling are not understood. The supply of essential inorganic nutrients to bacteroids in relation to nutrient partitioning in nodule tissues and nutrient transport to the symbiosome may affect effectiveness of nitrogen fixation. An integration of molecular approaches with more traditional biochemical, physiological and field-based studies is needed to improve understanding of the agricultural importance of rhizobia response to nutrient stress.

scholarly journals FixJ: a Major Regulator of the Oxygen Limitation Response and Late Symbiotic Functions of Sinorhizobium meliloti

2006 ◽  
Vol 188 (13) ◽  
pp. 4890-4902 ◽  
Author(s):  
Christine Bobik ◽  
Eliane Meilhoc ◽  
Jacques Batut
Keyword(s):  
Sinorhizobium Meliloti ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory System ◽  
Polyamine Metabolism ◽  
Nitrogen Fixing ◽  
Low Oxygen ◽  
Free Living ◽  
Expression Of Genes ◽  
Oxygen Conditions

ABSTRACT Sinorhizobium meliloti exists either in a free-living state in the soil or in symbiosis within legume nodules, where the bacteria differentiate into nitrogen-fixing bacteroids. Expression of genes involved in nitrogen fixation and associated respiration is governed by two intermediate regulators, NifA and FixK, respectively, which are controlled by a two-component regulatory system FixLJ in response to low-oxygen conditions. In order to identify the FixLJ regulon, gene expression profiles were determined in microaerobic free-living cells as well as during the symbiotic life of the bacterium for the wild type and a fixJ null-mutant strain. We identified 122 genes activated by FixJ in either state, including 87 novel targets. FixJ controls 74% of the genes induced in microaerobiosis (2% oxygen) and the majority of genes expressed in mature bacteroids. Ninety-seven percent of FixJ-activated genes are located on the symbiotic plasmid pSymA. Transcriptome profiles of a nifA and a fixK mutant showed that NifA activates a limited number of genes, all specific to the symbiotic state, whereas FixK controls more than 90 genes, involved in free-living and/or symbiotic life. This study also revealed that FixJ has no other direct targets besides those already known. FixJ is involved in the regulation of functions such as denitrification or amino acid/polyamine metabolism and transport. Mutations in selected novel FixJ targets did not affect the ability of the bacteria to form nitrogen-fixing nodules on Medicago sativa roots. From these results, we propose an updated model of the FixJ regulon.

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