Syntrophic exchange in synthetic microbial communities

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.Microbes are abundantly found in almost every part of the world, living in communities that are diverse in many facets. Although it is clear that cooperation and competition within microbial communities is central to their stability, maintenance, and longevity, there is limited knowledge about the general principles guiding the formation of these intricate systems. Understanding the underlying governing principles that shape a microbial community is key for microbial ecology but is also crucial for engineering synthetic microbiomes for various biotechnological applications (1–3). Numerous such examples have been recently described including the bioconversion of unprocessed cellulolytic feedstocks into biofuel isobutanol using fungal–bacterial communities (4) and biofuel precursor methyl halides using yeast–bacterial cocultures (5). Other emerging applications in biosensing and bioremediation against environmental toxins such as arsenic (6) and pathogens such as Pseudomonas aeruginosa and Vibrio cholerae have been demonstrated using engineered quorum-sensing Escherichia coli (7, 8). These advances paint an exciting future for the development of sophisticated multispecies microbial communities to address pressing challenges and the crucial need to understand the basic principles that enables their design and engineering.An important process that governs the growth and composition of microbial ecosystems is the exchange of essential metabolites, known as metabolic crossfeeding. Entomological studies have elucidated on a case-by-case basis the importance of amino acids in natural interkingdom and interspecies exchange networks (9–11). Recent comparative analyses of microbial genomes suggest that a significant proportion of all bacteria lack essential pathways for amino acid biosynthesis (2). These auxotrophic microbes thus require extracellular sources of amino acids for survival. Understanding amino acid exchange therefore presents an opportunity to gain new insights into basic principles in metabolic crossfeeding. Recently, several studies have used model systems of Saccharomyces cerevisiae (12), Saccharomyces enterica (13), and E. coli (14–16) to study syntrophic growth of amino acid auxotrophs in coculture environments. Numerous quantitative models have also been developed to describe the behavior of these multispecies systems, including those that integrate dynamics (17, 18), metabolism (19–21), and spatial coordination (22). Although these efforts have led to an improved understanding of the dynamics of syntrophic pairs and the energetic and benefits of cooperativity in these simple systems (23), larger more complex syntrophic systems have yet to be explored.Here, we use engineered E. coli mutants to study syntrophic crossfeeding, scaling to higher-dimensional synthetic ecosystems of increasing sophistication. We first devised pairwise syntrophic communities that show essential and interesting dynamics that can be predicted by simple kinetic models. We then increased the complexity of the interaction in three-member synthetic consortia involving crossfeeding of multiple metabolites. To further increase the complexity of our system, we devised a 14-member community to understand key drivers of population dynamics over short and evolutionary timescales. Finally, we provide evidence for widespread trends of metabolic crossfeeding based on comparative genomic analysis of amino acid biosynthesis across thousands of sequenced genomes. Our large-scale and systematic efforts represent an important foray into forward and reverse engineering synthetic microbial communities to gain key governing principles of microbial ecology and systems microbiology.     

Lead poisoning and the deceptive recovery of the critically endangered California condor

Endangered species recovery programs seek to restore populations to self-sustaining levels. Nonetheless, many recovering species require continuing management to compensate for persistent threats in their environment. Judging true recovery in the face of this management is often difficult, impeding thorough analysis of the success of conservation programs. We illustrate these challenges with a multidisciplinary study of one of the world's rarest birds-the California condor (Gymnogyps californianus). California condors were brought to the brink of extinction, in part, because of lead poisoning, and lead poisoning remains a significant threat today. We evaluated individual lead-related health effects, the efficacy of current efforts to prevent lead-caused deaths, and the consequences of any reduction in currently intensive management actions. Our results show that condors in California remain chronically exposed to harmful levels of lead; 30% of the annual blood samples collected from condors indicate lead exposure (blood lead ≥ 200 ng/mL) that causes significant subclinical health effects, measured as >60% inhibition of the heme biosynthetic enzyme δ-aminolevulinic acid dehydratase. Furthermore, each year, ～20% of free-flying birds have blood lead levels (≥450 ng/mL) that indicate the need for clinical intervention to avert morbidity and mortality. Lead isotopic analysis shows that lead-based ammunition is the principle source of lead poisoning in condors. Finally, population models based on condor demographic data show that the condor's apparent recovery is solely because of intensive ongoing management, with the only hope of achieving true recovery dependent on the elimination or substantial reduction of lead poisoning rates.     

Functional analysis of HIV type 1 Nef gene variants from adolescent and adult survivors of perinatal infection

Throughout the world, infants and children with HIV-1 infection are increasingly surviving into adolescence and adulthood. As HIV Nef is an important determinant of the pathogenic potential of the virus, we examined nef alleles in a cohort of extreme long-term survivors of HIV infection (average age of 16.6 years) to determine if Nef defects might have contributed to patient survival. HIV nef gene sequences were amplified for phylogenetic analysis from 15 adolescents and adults infected by mother-to-child transmission (n=10) or by blood transfusion (n=5). Functional analysis was performed by inserting patient-derived nef sequences into an HIV-derived vector that permits simultaneous evaluation of the impact of the Nef protein on MHC-I and CD4 cell surface expression. We found evidence of extensive nef gene diversity, including changes in known functional domains involved in the downregulation of cell surface MHC-I and CD4. Only 3 of 15 individuals (20%) had nef alleles with a loss of the ability to downregulate either CD4 or MHC-I. Survival into adulthood with HIV infection acquired in infancy is not uniformly linked to loss of function in nef. The Nef protein remains a potential target for immunization or pharmacologic intervention.     

The protein product of the proto-oncogene c-cbl forms a complex with phosphatidylinositol 3-kinase p85 and CD19 in anti-IgM-stimulated human B-lymphoma cells

Multiple signal transduction cascades, consisting of multiple interacting proteins, are activated following stimulation through most cell surface receptors, including the immunoglobulin receptor of B lymphocytes. In this report, we investigated the multimolecular complexes formed following anti-Ig stimulation of a human B-lymphoma cell line, resulting in activation of phosphatidylinositol 3-kinase (PI3K). PI3K is a lipid kinase that consists of an 85-kD regulatory subunit, bound to a 110-kD catalytic subunit. CD19 is a 95-kD B-cell surface marker that contains a consensus binding motif for PI3Kp85 in the cytoplasmic domain and recruits PI3K activity in activated B cells. The protein product of the c-cbl protooncogene is a 120-kD protein that is expressed in early B-lineage cells and in myeloid cells and is phosphorylated on tyrosine following receptor-mediated signaling in T and B lymphocytes. We demonstrate here that phosphorylated c-cbl complexes with CD19 and with PI3Kp85 via its C-terminal SH2 domain, and that both c-cbl and CD19 are associated with active PI3K in anti-Ig- stimulated cells. Although we cannot differentiate between a three- component, c-cbl/CD19/p85 complex and individual two-component complexes, these studies suggest that c-cbl may function as a docking protein, possibly linking distinct signal transduction pathways.     

Protein-tyrosine kinase p72syk in Fc gamma RI receptor signaling

In this report we show that gamma-interferon (IFN) induces the expression of the nonreceptor protein tyrosine kinase, p72syk, and that cross-linking the Fc gamma RI receptor in IFN-differentiated U937 cells (U937IF cells) results in the activation of syk kinase. We show that syk is tyrosine phosphorylated (12-fold increase) after Fc gamma RI cross-linking. In vitro kinase assays demonstrate that the specific kinase activity of syk increased eightfold after Fc gamma RI cross- linking. The activation of signal transduction through the Fc gamma RI receptor, as measured by the respiratory burst, is associated with the tyrosine phosphorylation and catalytic activation of the syk kinase. We show that syk coprecipitates with the gamma subunit of the Fc gamma RI, Fc gamma RI gamma. The data suggest that p72syk is involved in signal transduction through the Fc gamma RI receptor, involving the Fc gamma RI gamma subunit.