Search

Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m2/day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

Nitrobacter hamburgensis X14 is a facultative lithoautotroph that conserves energy from the oxidation of nitrite (N[O.sup.-.sub.2]) and fixes carbon dioxide (C[O.sub.2]) as its sole source of carbon. The availability of the N. hamburgensis X14 genorne sequence initiated a re-examination of its mixotrophic and organotrophic potential, as genes encoding three flavin-dependent oxidases were identified that may function to oxidize lactate, providing energy and carbon for growth. The response of N. harnburgensis to D- and L-lactate in the presence (mixotrophy) and absence (organotrophy) of N[O.sup.-.sub.2] was examined. L-Lactate did not support organotrophic growth or stimulate mixotrophic growth. In contrast, D-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of N[O.sup.-.sub.2], and served as the sole carbon and energy source for growth in the absence of N[O.sup.-.sub.2] with ammonium as the sole nitrogen source. Lithoautotrophically grown cells immediately consumed D-lactate, suggesting that a lactate metabolic pathway is constitutively expressed. Nevertheless, a physiological adaptation to lactate occurred, as D-lactate-grown cells consumed and assimilated lactate at a faster rate than N[O.sup.-.sub.2]-grown cells, and the D-lactate-dependent [O.sub.2] uptake rate was significantly greater in cells grown either organotrophically or mixotrophically compared with cells grown lithoautotrophically. Although D-lactate was assimilated and metabolized to C[O.sub.2] in the presence or absence of N[O.sup.-.sub.2], exposure to atmospheric C[O.sub.2] or the addition of 0.75 mM sodium carbonate was required for mixotrophic growth and for optimum organotrophic growth on D-lactate.

The genome sequencing and analysis of the alphaproteobacterium Nitrobacter winogradskyi revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. Approximately 10 percent of the Nitrobacter winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules.

Autophagy is a critical mechanism deployed by eukaryotic cells in response to stress, including viral infection, to boost the innate antimicrobial responses. However, an increasing number of pathogens hijack the autophagic machinery to facilitate their own replication. Influenza A virus (IAV), responsible for several global pandemics, has an intricate dependence on autophagy for successful replication in mammalian cells. To elucidate key chokepoints in the host stress responses facilitating IAV replication, we constructed a meta- transcriptome of IAV and host gene expression dynamics during early (1-3 hpi), mid (4-6 hpi), and late (8-12 hpi) stages of the viral replication cycle at two multiplicities of infection (MOI): 1 and 5. We supplemented the global transcriptome study with phosphoproteomic analysis of stress- activated protein kinase (SAPK/JNK) signaling in lung carcinoma (predominantly used as an in vitro model of IAV replication) and normal human bronchial epithelial cells. We report significant differences in the activation profiles of autophagy regulating genes upon IAV infection at the two MOI as well as divergent dependence on ULK1 signaling within the normal and cancer cells. Regardless of the cell model, JNK- Thr187 signaling was crucial for the production of infectious viral particles. [ABSTRACT FROM AUTHOR]

Legionella pneumophila type II secretion mutants have shown reduced survival in both tap water and aquatic amoebae. The analysis of these species has shown a correlation between low-temperature survival and secretion function.

A study was conducted to identify gene clusters of glycogen, polyphosphate, and cyanophycin storage and utilization which are responsible for mechanisms to meet energy requirements under substrate-limited conditions. The results obtained revealed that the genome of Nitrosomonas multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

Sequencing and analysis of the Nitrobacter hamburgensis X14 genome has shown four replicons comprised of one chromosome and three plasmids. Many of the subcore genes have diverged from the alphaproteobacterial lineage and have shown some of the unique genetic requirements for nitrite oxidation in Nitrobacter.

The article reports on a study which examines the ability of Nitrobacter hamburgensis to metabolize lactate and explores its effect on lithoautotrophy. According the study, the response of N. hamburgensis to D- and L-lactate in the presence of mixotrophy and absence of organotrophy of NO- 2 was examined. The study shows that the L-lactate did not support organotrophic growth or stimulate mixotrophic growth. In contrast, D-lactate enhanced the growth rate and yield of N. hamburgensis in the presence of NO- 2. The study suggests that lactate do not increase the rate of NO- 2 oxidation in N. hamburgensis, but instead lessens the NO- 2 requirement of the cell.

The filamentous cyanobacterium Microcoleus vaginatus is found in arid land soils worldwide. The genome of M. vaginatus strain FGP-2 allows exploration of genes involved in photosynthesis, desiccation tolerance, alkane production, and other features contributing to this organism's ability to function as a major component of biological soil crusts in arid lands. [ABSTRACT FROM AUTHOR]