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Sandhage, KH, Allan SM, Dickerson MB, Gaddis CS, Shian S, Weatherspoon MR, Cai Y, Ahmad G, Haluska MS, Snyder RL, Unocic RR, Zalar FM, Zhang YS, Rapp RA, Hildebrand M, Palenik BP.  2005.  Merging biological self-assembly with synthetic chemical tailoring: The potential for 3-D genetically engineered micro/nano-devices (3-D GEMS). International Journal of Applied Ceramic Technology. 2:317-326.   10.1111/j.1744-7402.2005.02035.x   AbstractWebsite

Appreciable global efforts are underway to develop processes for fabricating three-dimensional (3-D) nanostructured assemblies for advanced devices. Widespread commercialization of such devices will require: (i) precise 3-D fabrication of chemically tailored structures on a fine scale and (ii) mass production of such structures on a large scale. These often-conflicting demands can be addressed with a revolutionary new paradigm that couples biological self-assembly with synthetic chemistry: Bioclastic and Shape-preserving Inorganic Conversion (BaSIC). Nature provides numerous examples of microorganisms that assemble biominerals into intricate 3-D structures. Among the most spectacular of these microorganisms are diatoms (unicellular algae). Each of the tens of thousands of diatom species assembles silica nanoparticles into a microshell with a distinct 3-D shape and pattern of fine (nanoscale) features. The repeated doubling associated with biological reproduction enables enormous numbers of such 3-D microshells to be generated (e.g., only 40 reproduction cycles can yield >1 trillion 3-D replicas!). Such generic precision and massive parallelism are highly attractive for device manufacturing. However, the natural chemistries assembled by diatoms (and other microorganisms) are rather limited. With BaSIC processes, biogenic assemblies can be converted into a wide variety of new functional chemistries, while preserving the 3-D morphologies. Ongoing advances in genetic engineering promise to yield microorganisms tailored to assemble nanoparticle structures with device-specific shapes. Large-scale culturing of such genetically tailored microorganisms, coupled with shape-preserving chemical conversion (via BaSIC processes), would then provide low-cost 3-D Genetically Engineered Micro/nano-devices (3-D GEMs).

Shi, XG, Lin X, Li L, Li MZ, Palenik B, Lin SJ.  2017.  Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. Isme Journal. 11:2209-2218.   10.1038/ismej.2017.81   AbstractWebsite

Although gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress are still largely unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for Prorocentrum donghaiense to understand the molecular mechanisms by which this dinoflagellate copes with phosphorus (P) deficiency. Under P-depleted conditions, G1/S specific cyclin gene was markedly downregulated, consistent with growth inhibition, and genes related to dissolved organic phosphorus (DOP) hydrolysis, carbon fixation, nitrate assimilation, glycolysis, and cellular motility were upregulated. The elevated expression of ATP-generating genes (for example, rhodopsin) and ATP-consuming genes suggests some metabolic reconfiguration towards accelerated ATP recycling under P deficiency. MicroRNAome sequencing revealed 17 microRNAs, potentially regulating 3268 protein-coding genes. Functional enrichment analysis of these microRNA-targeted genes predicted decreases in sulfatide (sulfolipid) catabolism under P deficiency. Strikingly, we detected a significant increase in sulfolipid sulfatide content (but not in sulphoquinovosyldiacylglycerol content) and its biosynthesis gene expression, indicating a different sulfolipid-substituting-phospholipid mechanism in this dinoflagellate than other phytoplankters studied previously. Taken together, our integrative transcriptomic and microRNAomic analyses show that enhanced DOP utilization, accelerated ATP cycling and repressed sulfolipid degradation constitute a comprehensive strategy to cope with P deficiency in a model dinoflagellate.

Snyder, DS, Brahamsha B, Azadi P, Palenik B.  2009.  Structure of compositionally simple lipopolysaccharide from marine Synechococcus. Journal of Bacteriology. 191:5499-5509.   10.1128/jb.00121-09   AbstractWebsite

Lipopolysaccharide (LPS) is the first defense against changing environmental factors for many bacteria. Here, we report the first structure of the LPS from cyanobacteria based on two strains of marine Synechococcus, WH8102 and CC9311. While enteric LPS contains some of the most complex carbohydrate residues in nature, the full-length versions of these cyanobacterial LPSs have neither heptose nor 3-deoxy-D-manno-octulosonic acid (Kdo) but instead 4-linked glucose as their main saccharide component, with low levels of glucosamine and galacturonic acid also present. Matrix-assisted laser desorption ionization mass spectrometry of the intact minimal core LPS reveals triacylated and tetraacylated structures having a heterogeneous mix of both hydroxylated and nonhydroxylated fatty acids connected to the diglucosamine backbone and a predominantly glucose outer core-like region for both strains. WH8102 incorporated rhamnose in this region as well, contributing to differences in sugar composition and possibly nutritional differences between the strains. In contrast to enteric lipid A, which can be liberated from LPS by mild acid hydrolysis, lipid A from these organisms could be produced by only two novel procedures: triethylamine-assisted periodate oxidation and acetolysis. The lipid A contains odd-chain hydroxylated fatty acids, lacks phosphate, and contains a single galacturonic acid. The LPS lacks any limulus amoebocyte lysate gelation activity. The highly simplified nature of LPSs from these organisms leads us to believe that they may represent either a primordial structure or an adaptation to the relatively higher salt and potentially growth-limiting phosphate levels in marine environments.

Stuart, RK, Dupont CL, Johnson AD, Paulsen IT, Palenik B.  2009.  Coastal strains of marine synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. Applied and Environmental Microbiology. 75:5047-5057.   10.1128/aem.00271-09   AbstractWebsite

Copper appears to be influencing the distribution and abundance of phytoplankton in marine environments, and cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity. By using growth assays of phylogenetically divergent clades, we found that coastal strains of marine Synechococcus species were more tolerant to copper shock than open-ocean strains. The global transcriptional response to two levels of copper shock were determined for both a coastal strain and an open-ocean strain of marine Synechococcus species using whole-genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus species. The two strains additionally showed a common reduction in levels of photosynthesis-related gene transcripts. Contrastingly, the open-ocean strain showed a general stress response, whereas the coastal strain exhibited a more specifically oxidative or heavy-metal acclimation response that may be conferring tolerance. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus strains may in part be a result of a generally increased ability to sense and respond in a more stress-specific manner.

Stuart, RK, Brahamsha B, Busby K, Palenik B.  2013.  Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress. Isme Journal. 7:1139-1149.   10.1038/ismej.2012.175   AbstractWebsite

Highly variable regions called genomic islands are found in the genomes of marine picocyano-bacteria, and have been predicted to be involved in niche adaptation and the ecological success of these microbes. These picocyanobacteria are typically highly sensitive to copper stress and thus, increased copper tolerance could confer a selective advantage under some conditions seen in the marine environment. Through targeted gene inactivation of genomic island genes that were known to be upregulated in response to copper stress in Synechococcus sp. strain CC9311, we found two genes (sync_1495 and sync_1217) conferred tolerance to both methyl viologen and copper stress in culture. The prevalence of one gene, sync_1495, was then investigated in natural samples, and had a predictable temporal variability in abundance at a coastal monitoring site with higher abundance in winter months. Together, this shows that genomic island genes can confer an adaptive advantage to specific stresses in marine Synechococcus, and may help structure their population diversity.

Stuart, RK, Bundy R, Buck K, Ghassemain M, Barbeau K, Palenik B.  2017.  Copper toxicity response influences mesotrophic Synechococcus community structure. Environmental Microbiology. 19:756-769.   10.1111/1462-2920.13630   AbstractWebsite

Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, species', also known as clades. Here, we compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbour stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.

Su, ZC, Mao FL, Dam P, Wu HW, Olman V, Paulsen IT, Palenik B, Xu Y.  2006.  Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp WH 8102. Nucleic Acids Research. 34:1050-1065.   10.1093/nar/gkj496   AbstractWebsite

Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.

Swift, H, Palenik B.  1993.  Prochlorophyte evolution and the origin of chloroplasts: Morphological and molecular evidence. Origins of plastids : symbiogenesis, prochlorophytes, and the origins of chloroplasts. ( Lewin RA, Ed.).:123-139., New York: Chapman & Hall Abstract