Evolution of root endosymbiosis with bacteria: How novel are nodules?

Medicago truncatula proteomics

Legumes (Fabaceae) are unique in their ability to enter into an elaborate symbiosis with nitrogen-fixing rhizobial bacteria. Rhizobia-legume (RL) symbiosis represents one of the most productive nitrogen-fixing systems and effectively renders the host plants to be more or less independent of other nitrogen sources. Due to high protein content, legumes are among the most economically important crop families. Beyond that, legumes consist of over 16,000 species assigned to 650 genera. In most cases, the genomes of legumes are large and polyploid, which originally did not predestine these plants as genetic model systems. It was not until the early 1990 th that Medicago truncatula was selected as the model plant for studying Fabaceae biology. M. truncatula is closely related to many economically important legumes and therefore its investigation is of high relevance for agriculture. Recently, quite a number of studies were published focussing on in depth characterizations of the M. truncatula proteome. The present review aims to summarize these studies, especially those which focus on the root system and its dynamic changes induced upon symbiotic or pathogenic interactions with microbes.

A dominant function of CCaMK in intracellular accommodation of bacterial and fungal endosymbionts

In legumes, Ca(2+)/calmodulin-dependent protein kinase (CCaMK) is a component of the common symbiosis genes that are required for both root nodule (RN) and arbuscular mycorrhiza (AM) symbioses and is thought to be a decoder of Ca(2+) spiking, one of the earliest cellular responses to microbial signals. A gain-of-function mutation of CCaMK has been shown to induce spontaneous nodulation without rhizobia, but the significance of CCaMK activation in bacterial and/or fungal infection processes is not fully understood. Here we show that a gain-of-function CCaMK(T265D) suppresses loss-of-function mutations of common symbiosis genes required for the generation of Ca(2+) spiking, not only for nodule organogenesis but also for successful infection of rhizobia and AM fungi, demonstrating that the common symbiosis genes upstream of Ca(2+) spiking are required solely to activate CCaMK. In RN symbiosis, however, CCaMK(T265D) induced nodule organogenesis, but not rhizobial infection, on Nod factor receptor (NFRs) mutants. We propose a model of symbiotic signaling in host legume plants, in which CCaMK plays a key role in the coordinated induction of infection thread formation and nodule organogenesis.

Plants versus pathogens: an evolutionary arms race

The analysis of plant-pathogen interactions is a rapidly moving research field and one that is very important for productive agricultural systems. The focus of this review is on the evolution of plant defence responses and the coevolution of their pathogens, primarily from a molecular-genetic perspective. It explores the evolution of the major types of plant defence responses including pathogen associated molecular patterns and effector triggered immunity as well as the forces driving pathogen evolution, such as the mechanisms by which pathogen lineages and species evolve. Advances in our understanding of plant defence signalling, stomatal regulation, R gene-effector interactions and host specific toxins are used to highlight recent insights into the coevolutionary arms race between pathogens and plants. Finally, the review considers the intriguing question of how plants have evolved the ability to distinguish friends such as rhizobia and mycorrhiza from their many foes.

Inactivation of duplicated nod factor receptor 5 (NFR5) genes in recessive loss-of-function non-nodulation mutants of allotetraploid soybean (Glycine max L. Merr.)

Chemically induced non-nodulating nod139 and nn5 mutants of soybean (Glycine max) show no visible symptoms in response to rhizobial inoculation. Both exhibit recessive Mendelian inheritance suggesting loss of function. By allele determination and genetic complementation in nod139 and nn5, two highly related lipo-oligochitin LysM-type receptor kinase genes in Glycine max were cloned; they are presumed to be the critical nodulation-inducing (Nod) factor receptor similar to those of Lotus japonicus, pea and Medicago truncatula. These duplicated receptor genes were called GmNFR5alpha and GmNFR5beta. Nonsense mutations in GmNFR5alpha and GmNFR5beta were genetically complemented by both wild-type GmNFR5alpha and GmNFR5beta in transgenic roots, indicating that both genes are functional. Both genes lack introns. In cultivar Williams82 GmNFR5alpha is located in chromosome 11 and in tandem with GmLYK7 (a related LysM receptor kinase gene), while GmNFR5beta is in tandem with GmLYK4 in homologous chromosome 1, suggesting ancient synteny and regional segmental duplication. Both genes are wild type in G. soja CPI100070 and Harosoy63; however, a non-functional NFR5beta allele (NFR5beta*) was discovered in parental lines Bragg and Williams, which harbored an identical 1,407 bp retroelement-type insertion. This retroelement (GmRE-1) and related sequences are located in several soybean genome positions. Paradoxically, putatively unrelated soybean cultivars shared the same insertion, suggesting a smaller than anticipated genetic base in this crop. GmNFR5alpha but not GmNFR5beta* was expressed in inoculated and uninoculated tap and lateral root portions at about 10-25% of GmATS1 (ATP synthase subunit 1), but not in trifoliate leaves and shoot tips.

Symbiont genomics, our new tangled bank

Microbial symbionts inhabit the soma and surfaces of most multicellular species and instigate both beneficial and harmful infections. Despite their ubiquity, we are only beginning to resolve major patterns of symbiont ecology and evolution. Here, we summarize the history, current progress, and projected future of the study of microbial symbiont evolution throughout the tree of life. We focus on the recent surge of data that whole-genome sequencing has introduced into the field, in particular the links that are now being made between symbiotic lifestyle and molecular evolution. Post-genomic and systems biology approaches are also emerging as powerful techniques to investigate host-microbe interactions, both at the molecular level of the species interface and at the global scale. In parallel, next-generation sequencing technologies are allowing new questions to be addressed by providing access to population genomic data, as well as the much larger genomes of microbial eukaryotic symbionts and hosts. Throughout we describe the questions that these techniques are tackling and we conclude by listing a series of unanswered questions in microbial symbiosis that can potentially be addressed with the new technologies.

Differential gel electrophoresis (DIGE) to quantitatively monitor early symbiosis- and pathogenesis-induced changes of the Medicago truncatula root proteome

Symbiosis- and pathogenesis-related early protein induction patterns in the model legume Medicago truncatula were analysed with two-dimensional differential gel electrophoresis. Two symbiotic soil microorganisms (Glomus intraradices, Sinorhizobium meliloti) were used in single infections and in combination with a secondary pathogenic infection by the oomycete Aphanomyces euteiches. Proteomic analyses performed 6 and 24h after inoculations led to identification of 87 differentially induced proteins which likely represent the M. truncatula root 'interactome'. A set of proteins involved in a primary antioxidant defense reaction was detected during all associations investigated. Symbiosis-related protein induction includes a typical factor of early symbiosis-specific signalling (CaM-2), two Ran-binding proteins of nucleocytoplasmic signalling, and a set of energy-related enzymes together with proteins involved in symbiosis-initiated C- and N-fixation. Pathogen-associated protein induction consists of mainly PR proteins, Kunitz-type proteinase inhibitors, a lectin, and proteins related to primary carbohydrate metabolism and phytoalexin synthesis. Absence of PR proteins and decreased pathogen-induced protein patterns during mixed symbiotic and pathogenic infections indicate bioprotective effects due to symbiotic co-infection. Several 14-3-3 proteins were found as predominant proteins during mixed infections. With respect to hormone-regulation, A. euteiches infection led to induction of ABA-related pathways, while auxin-related pathways are induced during symbiosis.