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Bradyrhizobium Japonicum Genes for Life in Specific Hosts Research Collection Doctoral Thesis Bradyrhizobium japonicum genes for life in specific hosts Author(s): Koch, Marion Publication Date: 2011 Permanent Link: https://doi.org/10.3929/ethz-a-006410064 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH No. 19577 Bradyrhizobium japonicum genes for life in specific hosts A dissertation submitted to the ETH Zürich for the degree of DOCTOR OF SCIENCES presented by MARION KOCH Dipl. Biol., Universität Konstanz born on January 1st, 1983 citizen of Germany Prof. Dr. Hauke Hennecke, examiner Dr. Gabriella Pessi, co-examiner Prof. Dr. Thomas Boller, co-examiner Prof. Dr. Julia Vorholt, co-examiner Prof. Dr. Samuel Zeeman, co-examiner 2011 Table of contents Thesis summary 1 Zusammenfassung 3 Chapter 1: Introduction 7 1.1 Rhizobia and Bradyrhizobium japonicum 8 Historical overview 8 Bradyrhizobium japonicum 8 Nitrogen fixation 9 1.2 Molecular basis of the rhizobia-legume symbiosis 11 Legume flavonoids 11 Rhizobial Nod factors 11 Nod factor perception in legume roots 13 Plant responses to Nod factors 14 Formation of a root nodule 15 1.3 Global strategies to monitor rhizobial gene and protein expression in symbiosis 18 1.4 Host specificity 25 NodD proteins 25 Other nod genes as host-specific determinants 26 Polysaccharides and secreted proteins as host-specific determinants 26 Cultivar specificity 27 Host-specific adaptation 28 1.5 Carbon metabolism in rhizobia 30 Carbon metabolism in free-living rhizobia 30 Carbon metabolism in symbiotic rhizobia 32 Oxalotrophic bacteria 35 1.6 Aim of this work 40 Chapter 2: Characterization of two carbonic anhydrase genes 41 2.1 Abstract 42 2.2 Introduction 43 2.3 Material and methods 46 Bacterial strains, media and growth conditions 46 DNA work 46 Construction of Δbll2065-2066 deletion and bll4865::pRJ6226 insertion mutants 47 Plant growth 49 Quantitative real-time PCR 49 2.4 Results 50 Bradyrhizobium japonicum possesses five carbonic anhydrase genes 50 Construction of mutations in two β carbonic anhydrase genes bll2065 and bll4865 51 Symbiotic phenotype of ∆bll2065-2066 and bll4865::pRJ6226 strains 53 Expression studies of B. japonicum carbonic anhydrase genes 54 2.5 Discussion 56 Chapter 3: Rhizobial adaptation to hosts, a new facet in the legume root- 59 nodule symbiosis 3.1 Abstract 60 3.2 Introduction 61 3.3 Results and discussion 64 Transcriptome analysis of B. japonicum in root nodules of cowpea, siratro, and 64 soybean Proteome analysis of bacteroids from cowpea, siratro, and soybean nodules 65 The stringent data set: where host-specific transcriptomes and proteomes overlap 67 An approved determinant for bacteroid adaptation to life in siratro nodules 67 In search for the substrate of Bll1600-1604 73 Further candidates with a perspective to act in a host-responsive manner 75 The relaxed data set: transcriptomes and proteomes combined 76 3.4 Concluding remarks 78 3.5 Material and methods 79 DNA methods and construction of mutant strains 79 Phenotypic MicroArray tests 81 Growth and sensitivity assays 81 Plant material, inoculation, and growth conditions 81 Transcriptome analyses 82 Proteome analyses 83 3.6 Addendum: Further candidates with a perspective to act in a host-responsive 86 manner Results and discussion 86 Mutant construction 88 Chapter 4: Oxalotrophy in Bradyrhizobium japonicum 89 4.1 Abstract 90 4.2 Introduction 91 4.3 Material and methods 94 Bacterial strains, media and growth conditions 94 Oxalotrophic growth 94 Isothermal calorimetry 95 DNA methods and construction of mutant strains 96 Symbiotic growth analysis: Plant material, inoculation and cultivation 98 Determination of the oxalate content of roots and nodules of soybean, mungbean, 98 cowpea and sirato infected with B. japonicum 4.4 Results 100 Identification and transcriptional analysis of the frc, oxc genomic region 100 Construction of ∆oxlT1+2 and ∆frc-oxc deletion mutants 102 Free-living growth analysis in presence of various carbon sources 102 Oxalate content in roots and root nodules induced by B. japonicum 105 Symbiotic properties of the ∆frc-oxc and ∆oxlT1+2 mutants 106 4.5 Discussion 107 4.6 Addendum: Competitiveness in symbiosis 112 Chapter 5: Future perspectives 113 5.1 Characterization of two β-class carbonic anhydrase (CA) genes 114 5.2 Host-specific adaptation 116 5.3 Oxalotrophy in B. japonicum 118 References 121 Publications 131 Curriculum vitae 133 Acknowledgements 135 Thesis summary Thesis summary Bradyrhizobium japonicum is able to either persist as a free-living bacterium in soil or laboratory cultures or to enter a symbiosis with various legume plants such as soybean, mungbean, cowpea and siratro. These symbiotic interactions result in the formation of nodules at the roots of their hosts. At the heart of these symbioses is the ability of the bacterial endosymbiont to reduce atmospheric nitrogen to ammonia, which is given to and used by the plant. This natural fertilization enables legume plants to grow on nitrogen-poor soil. In return, the bacterium is supplied with carbon sources such as succinate generated by the symbiotic partner as a consequence of photosynthetic CO2 fixation. The first part of this thesis deals with the characterization of a carbonic anhydrase gene (bll2065) which was previously discovered to be specifically and highly expressed during symbiosis of B. japonicum with soybean when compared to free-living aerobically grown cells (Pessi et al. 2007). A complementary proteomics approach recently showed that a second B. japonicum carbonic anhydrase, Bll4865, was also expressed during soybean symbiosis (Delmotte et al. 2010). Therefore, we decided to characterize these two carbonic anhydrase genes. Although these genes are expressed in bacteroids, mutant analysis showed that each of them by itself is not essential for B. japonicum to successfully enter and establish a nitrogen fixing symbiosis with its soybean host. In the second part, we aimed at monitoring global gene expression changes of B. japonicum in response to different host environments. To achieve this goal, we analyzed the transcriptome as well as the proteome of B. japonicum bacteroids in root nodules from soybean, cowpea and siratro. These analyses revealed that B. japonicum bacteroids indeed 1 Thesis summary respond partly disparately in gene expression, depending on who is the symbiotic plant partner. In total two genes/proteins for cowpea, five for siratro, and seven for soybean were identified. One gene cluster for a predicted ABC-type transporter (blr1601-1604) plus a monooxygenase (blr1600) was identified to be specifically expressed during symbiosis with siratro. Mutant analysis showed that this operon is indeed more important for the B. japonicum-siratro symbiosis than for the symbiosis with soybean and cowpea. Complementation analysis revealed that the monooxygenase gene (blr1600) alone cannot compensate the host-specific deletion mutant phenotype on siratro. At least one of the ABC transporter genes is needed for successful complementation. Thus, based on two global studies, we could identify a host-specific adaptation determinant for B. japonicum. Finally, a third part of this work was dedicated to gain insight into a particular aspect of carbon catabolism of B. japonicum. Based on genome annotation and microarray data, B. japonicum possesses and expresses genes for the uptake and metabolism of oxalate. Similar genes were previously shown to be important for the oxalotrophic lifestyle of bacteria such as Oxalobacter formigenes. We showed here that B. japonicum is able to use the C2 compound oxalate as the sole source of carbon. Moreover, mutant analysis indicated that the genes frc (coding for a formyl-CoA transferase) and oxc (coding for an oxalyl-CoA transferase) are essential for oxalate degradation. Interestingly, a preliminary analysis suggested that frc and oxc are important for competition for nodule occupancy. The ability to degrade oxalate might confer an advantage for B. japonicum during the establishment of a symbiosis with legume plants. 2 Zusammenfassung Zusammenfassung Bradyrhizobium japonicum ist einerseits fähig, als frei lebendes Bakterium im Erdboden sowie in Laborkulturen zu existieren, und kann andererseits Symbiosen mit diversen Hülsenfrüchtlern wie beispielsweise Sojabohnen, Mungbohnen, Langbohnen und Siratro eingehen. Die symbiotische Wechselbeziehung bewirkt die Ausbildung von Knöllchen an den Wurzeln der Hülsenfrüchtler. Von zentraler Bedeutung bei der Symbiose ist die Fähigkeit des bakteriellen Endosymbioten, atmosphärischen Stickstoff in Ammonium umzuwandeln, welcher dann der Pflanze zur Verfügung gestellt und von ihr verwertet wird. Dieser natürliche Düngungsprozess ermöglicht es genannten Hülsenfrüchtlern auch auf stickstoffarmen Böden zu gedeihen. Als Gegenleistung wird das Bakterium in der Symbiose mit Kohlenstoffquellen wie beispielsweise Succinat versorgt, welche die Hülsenfrüchtler als Konsequenz der photosynthetischen CO2-Fixierung erzeugen. Der erste Teil dieser Arbeit beschäftigt sich mit der Charakterisierung eines Carboanhydrase- Gens (bll2065), welches man bei einer vorhergehenden Studie identifiziert hat. Jene Arbeit widmete sich der Identifizierung von Genen, welche in B. japonicum während der Symbiose mit Sojabohnen im Vergleich zu freilebenden, aerob gezüchteten Zellen hoch exprimiert waren (Pessi et al. 2007). Bei einer komplementären Studie,
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