MICROBIAL PARTNERS IN HEALTH: BROADENING OUR UNDERSTANDING OF HOST-MICROBIOME RELATIONSHIPS

While microbes inhabit a wide array of environments, their ability to live within host tissue and become tolerated as part of a select microbial community is perhaps one of the most impressive feats of microbial resilience and survival. Host microbiome establishment and maintenance requires both host-microbe and microbe-microbe interactions. Among plant hosts, benefits from associated microbiomes are known to include improved growth, development and resistance to abiotic and biotic stresses. Mammalian microbiomes are known to improve host digestion, influence inflammation and even improve immune response to pathogens. While host-associated microbial communities across all domains of life are incredibly diverse, a growing number of studies are finding host-specific taxonomic trends, suggesting microbiome conservation and evolutionary selection. However, we have come to recognize that there is often functional redundancy between taxa. Therefore, investigative focus on microbiome composition potentially neglects pivotal and influential microbial players. Shifting focus to function over form creates the opportunity to tease apart the driving forces of unique microbiome constituents. This allows for identification of strains and genes of interest as well as microbial selections. To that end, here we describe the relationships between hosts and microbiomes as well as between microbes in two vastly different host systems (Figure 1.1). First, we suggest that plant root-associated Streptomyces isolates harboring genes encoding an enzyme and its co-factor are more tolerant of phenolic compounds generated by roots. Next, we address the capability of these Streptomyces isolates to employ their metabolic repertoires to influence the composition of the root microbiome. Finally, we define a previously under-described role for the gut microbiome in malaria immunology and suggest that gut microbial composition can modulate the severity of malarial disease. Together, these findings demonstrate the broad implications of microbiome composition across diverse hosts and environments, revealing unexplored opportunities for therapeutic interventions aimed at improving plant and human health

Transcriptome Analysis of Root Development in Wheat \u3cem\u3e Triticum Aestivum\u3c/em\u3e Using High Throughtput Sequencing Technologies

Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were successfully assembled into ~91K transcripts coding for functional proteins. Of these ~91K transcripts, 1,728 were differentially expressed in root tip as compared to the rest of the mature tissues. Generation of the root reference transcriptome and the availability of a reasonable reference genome sequence for wheat enabled us to analyze the gene expression in the long root (LR) and VSR. A total of 4,412 genes were differentially expressed in the VSR compared to the LR root tips. A significant portion of the differentially expressed genes functioning in the hormonal responses, regulation of transcription, defense response, reactive oxygen species (ROS), abiotic stress response, lignin biosynthesis, calcium signaling, and autophagy pathways were induced. In addition, several negative regulators of cell proliferation, including homologs of the BIGBROTHER E3 ubiquitin ligase, and negative regulators of root cell elongation, such as genes encoding the FERONIA kinases and a RALF peptide hormone, were also up-regulated in VSR. Consistent with this, a large number of genes for chromatin replication and protein syntheses, including those coding for histones and ribosomal proteins, and cell wall remodeling enzymes, were down-regulated in VSR. The ROS and lignin accumulation in the VSR were further validated by histochemical staining. This research revealed several molecular mechanisms of root development, based on which a working model was proposed to explain the VSR development. Although the related pathways identified in Arabidopsis may play a similar role in wheat, the VSR phenotype is probably governed by a unique mechanism that may be cereal- or wheat-specific

Origin of Gene Specificity in the Nitrogen-Fixing Symbiosis

Many legumes form a symbiosis with nitrogen-fixing bacteria found in the soil. This relationship is beneficial to both the plant and the bacteria; the plant receives nitrogen that is otherwise limited, and the bacteria receive fixed carbon. Upon sensing the bacteria, the plant forms a new organ (the nodule) where the bacteria are housed within the cells. Many genes are required for the proper formation and function of nodules; this dissertation is broadly focused on how genes required for nitrogen-fixing symbiosis are co-opted from other cellular processes and how they are specialized for symbiosis. Protein trafficking from the plant to the intracellular bacteria is critical to the success of the symbiosis. This protein trafficking is the cellular anterograde secretory pathway repurposed toward a new intracellular compartment. In the model legume Medicago truncatula, a deletion in DNF1, which encodes the nodule-specific 22kDa signal peptidase complex (SPC) subunit, causes the nodules to be unable to fix nitrogen because the nodule-specific protein trafficking machinery disrupted. Here, we have shown that DNF1 became specialized in symbiosis through nodule-specific expression, and we identify cis-elements that are crucial for that transcriptional control in the DNF1 promoter and other SPC subunit genes. Furthermore, we have found that another protein trafficking protein, SYP132A, was co-opted from arbuscular mycorrhizal symbiosis for its role in nitrogen-fixing symbiosis. This t-SNARE is localized to the symbiotic membranes in both symbioses and is required for proper arbuscule and bacteroid development within host cells. One class of proteins that are specifically targeted to the symbiosome are nodule-specific cysteine-rich (NCR) peptides, which are involved in the differentiation of the intracellular bacteria. In general, NCR peptides are required for nitrogen fixation in Medicago, but their specific modes of action are largely unknown. Here, we describe and characterize two NCR motifs that are found in many different peptides, pointing to a common, conserved amino acid sequence, possibly contributing to the efficacy of these peptides. Finally, we show that the receptor, DMI2, which is required for rhizobia infection, is regulated at the protein level in Medicago. DMI2 is constitutively expressed, but in the absence of rhizobia infection, it is degraded by the proteasome. During infection, however, it is protected from degradation, and the protein accumulates

26th Fungal Genetics Conference at Asilomar

Program and abstracts from the 26th Fungal Genetics Conference, March 15-20, 2011

Immunity and physiology of Lepidoptera is influenced by midgut mediated environmental signals

Die meisten Organismen auf der Erde werden von Pathogenen bedroht. Um sich gegen Pathogene zu schützen, haben Organismen ein oftmals komplexes Immunsystem entwickelt. Das Immunsystem hat viele unterschiedene Zellulare und Humorale Komponenten. Verschiedene Komponenten des Immunrepertoires sind aktiv gegen unterschiedliche Pathogene und haben daher unterschiedliche Kosten für den Organismus. Das führt zu einen komplexen Muster von trade-offs und anderen life-history Eigenschaften wie zum Beispiel Auswirkungen auf Lebenslänge und Reproduktion. Die Verteilung von Rohstoffen zwischen Immunität und anderen lebenswichtigen Funktionen hat einen substantiellen Einfluss auf die generelle Fitness des Organismus. Eine Investition in Immunität ist nur dann positiv für die Fitness, wenn ein reales Risiko für einen Pathogenbefall besteht. Die Frage besteht also, ob es möglich ist, die Pathogenität der Umwelt wahrzunehmen und den eigenen Immunstatus entsprechend zu ändern. Eine der primären Interaktionsflächen zwischen der Umwelt und der Lepidopteren-Raupe ist das Verdauungssystem. Viele bakterielle Infektionen, wie zum Beispiel Bacillus thuringiensis, fangen im Larvendarm bei der Verdauung an. Das heisst, dass der Darm die Grenzfläche für potentielle Immunsignale und somit den Informationsaustausch über mögliche Infektionen und die Vorbereitung des Immunsystems darstellt. Das Wissen über Immunsignalwege und Moleküle, die in der Immunantwort eine Rolle spielen, ist in den letzten Jahren erheblich gewachsen. Gleichzeitig ist nicht sehr viel über die Umweltfaktoren, die die Entwicklung des Immunsystems beeinflussen können, bekannt. Bis zum heutigen Tag gibt es keine einzige Studie über die Wirkung von nicht-pathogenen Bakterien, die von Insekten mit dem Futter aufgenommen werden, auf das Immunsystem

Comparative genomic analysis of Ralstonia solanacearum species complex

Ralstonia solanacearum species complex (RSSC) consist of a group of phytopathogenic bacteria that can infect many economically important crops, including tomatoes, potatoes, and bananas. RSSC are very diverse, capable of surviving up to 200 plant host species and various environmental reservoirs such as soils, river water and secondary wild plant hosts. The diversity of the RSSC is often credited to its large bipartite genome (5-6Mbp), that encodes multiple genes linked to virulence and survival across different niches. In this thesis, I investigated the genetic diversity of RSSC at worldwide (55 countries), country (the UK) and crop field (four tomato fields in China) levels. Worldwide, we found that the open pangenome of RSSC contained 18,080 genes. I estimate that the recombination across the phylogeny occurred five times frequently than mutation. Moreover, I show that insertion sequences linked to virulence and metal resistance genes played an important role in the accessory genome diversification of RSSC. Within the UK, I show that the diversification of the clonal phylotype IIB-1 strain is due to initial loss of accessory genes and movement of IS elements with estimated origin of the population dated between 1958 and 1988. At the field level, we show that two to three clonal lineages co-occur within all sampled fields. Interestingly, co-occurring lineages differ in their virulence traits and gene content, which could be due to due to adaptation to different niches within each field. The work presented here lays the groundwork for a systematic understanding of the ecological and evolutionary genomics of the RSSC species complex, at the local and global scale. It also demonstrates that instead of mutations, recombination and highly mobile transposases are important drivers of RSSC genetic diversity