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Collier, JL, Brahamsha B, Palenik B.  1999.  The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amidohydrolase, EC to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme. Microbiology-Sgm. 145:447-459.   10.1099/13500872-145-2-447   AbstractWebsite

Cyanobacteria assigned to the genus Synechococcus are an important component of oligotrophic marine ecosystems, where their growth may be constrained by low availability of fixed nitrogen. Urea appears to be a major nitrogen resource in the sea, but little molecular information exists about its utilization by marine organisms, including Synechococcus. Oligonucleotide primers were used to amplify a conserved fragment of the urease (urea amidohydrolase, EC coding region from cyanobacteria. A 5.7 kbp region of the genome of the unicellular marine cyanobacterium Synechococcus sp. strain WH7805 was then cloned, and genes encoding three urease structural subunits and four urease accessory proteins were sequenced and identified by homology. The WH7805 urease had a predicted subunit composition typical of bacterial ureases, but the organization of the WH7805 urease genes was unique. Biochemical characteristics of the WH7805 urease enzyme were consistent with the predictions of the sequence data. Physiological data and sequence analysis both suggested that the urease operon may be nitrogen-regulated by the ntcA system in WH7805. Inactivation of the large subunit of urease, ureC, prevented WH7805 and Synechococcus WH8102 from growing on urea, demonstrating that the urease genes cloned are essential to the ability of these cyanobacteria to utilize urea as a nitrogen source.

Keeling, PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, Armbrust VE, Archibald JM, Bharti AK, Bell CJ, Beszteri B, Bidle KD, Cameron CT, Campbell L, Caron DA, Cattolico RA, Collier JL, Coyne K, Davy SK, Deschamps P, Dyhrman ST, Edvardsen B, Gates RD, Gobler CJ, Greenwood SJ, Guida SM, Jacobi JL, Jakobsen KS, James ER, Jenkins B, John U, Johnson MD, Juhl AR, Kamp A, Katz LA, Kiene R, Kudryavtsev A, Leander BS, Lin S, Lovejoy C, Lynn D, Marchetti A, McManus G, Nedelcu AM, Menden-Deuer S, Miceli C, Mock T, Montresor M, Moran MA, Murray S, Nadathur G, Nagai S, Ngam PB, Palenik B, Pawlowski J, Petroni G, Piganeau G, Posewitz MC, Rengefors K, Romano G, Rumpho ME, Rynearson T, Schilling KB, Schroeder DC, Simpson AGB, Slamovits CH, Smith DR, Smith JG, Smith SR, Sosik HM, Stief P, Theriot E, Twary SN, Umale PE, Vaulot D, Wawrik B, Wheeler GL, Wilson WH, Xu Y, Zingone A, Worden AZ.  2014.  The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12:e1001889.: Public Library of Science   10.1371/journal.pbio.1001889   AbstractWebsite

Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

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).

Roulier, MA, Palenik B, Morel FMM.  1990.  A method for the measurement of choline and hydrogen-peroxide in seawater. Marine Chemistry. 30:409-421.   10.1016/0304-4203(90)90084-p   AbstractWebsite

The horseradish peroxidase-mediated dimerization of hydroxyphenylpropionic acid can be used to measure hydrogen peroxide in seawater. The method was optimized and interferences investigated, and the method was then adapted to the measurement of choline in seawater. The enzyme choline oxidase is used specifically to oxidize choline to produce betaine and H2O2, and the latter is measured. Possible interferences with this method were investigated, and choline was measured in coastal seawater, where it varied from 0 to 45 nM.

Wang, SY, Lambert W, Giang S, Goericke R, Palenik B.  2014.  Microalgal assemblages in a poikilohaline pond. Journal of Phycology. 50:303-309.   10.1111/jpy.12158   AbstractWebsite

Microalgal strains for algal biofuels production in outdoor ponds will need to have high net growth rates under diverse environmental conditions. A small, variable salinity pond in the San Elijo Lagoon estuary in southern California was chosen to serve as a model pond due to its routinely high chlorophyll content. Profiles of microalgal assemblages from water samples collected from April 2011 to January 2012 were obtained by constructing 18S rDNA environmental clone libraries. Pond assemblages were found to be dominated by green algae Picochlorum sp. and Picocystis sp. throughout the year. Pigment analysis suggested that the two species contributed most of the chlorophyll a of the pond, which ranged from 21.9 to 664.3 mu g center dot L-1 with the Picocystis contribution increasing at higher salinities. However, changes of temperature, salinity or irradiance may have enabled a bloom of the diatom Chaetoceros sp. in June 2011. Isolates of these microalgae were obtained and their growth rates characterized as a function of temperature and salinity. Chaetoceros sp. had the highest growth rate over the temperature test range while it showed the most sensitivity to high salinity. All three strains showed the presence of lipid bodies during nitrogen starvation, suggesting they have potential as future biofuels strains.

Tetu, SG, Brahamsha B, Johnson DA, Tai V, Phillippy K, Palenik B, Paulsen IT.  2009.  Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp WH8102. ISME Journal. 3:835-849.   10.1038/ismej.2009.31   AbstractWebsite

Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria, is often limited by low inorganic phosphate (P). To observe how these organisms cope with P starvation, we constructed a full genome microarray for Synechococcus sp. WH8102 and compared differences in gene expression under P-replete and P-limited growth conditions, including both early P stress, during extracellular alkaline phosphatase induction, and late P stress. A total of 36 genes showed significant upregulation (>log(2) fold) whereas 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained during late P stress for only 5 of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 and SYNW0948, comprising a two-component regulator hypothesized to have a key function in regulating P metabolism. A high degree of overlap in the sets of genes affected by P stress conditions and in the knockout mutants supports this hypothesis; however, there is some indication that other regulators may be involved in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria. The ISME Journal (2009) 3, 835-849; doi: 10.1038/ismej.2009.31; published online 2 April 2009

Dupont, CL, Yang S, Palenik B, Bourne PE.  2006.  Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry. Proceedings of the National Academy of Sciences of the United States of America. 103:17822-17827.   10.1073/pnas.0605798103   AbstractWebsite

Because of the rise in atmospheric oxygen 2.3 billion years ago (Gya) and the subsequent changes in oceanic redox state over the last 2.3-1 Gya, trace metal bioavailability in marine environments has changed dramatically. Although theorized to have influenced the biological usage of metals leaving discernable genomic signals, a thorough and quantitative test of this hypothesis has been lacking. Using structural bioinformatics and whole-genome sequences, the Fe-, Zn-, Mn-, and Co-binding metallomes of 23 Archaea, 233 Bacteria, and 57 Eukarya were constructed. These metallomes reveal that the overall abundances of these metal-binding structures scale to proteome size as power laws with a unique set of slopes for each Superkingdom of Life. The differences in the power describing the abundances of Fe-, Mrl Zn-, and Co-binding proteins in the proteomes of Prokaryotes and Eukaryotes are similar to the theorized changes in the abundances of these metals after the oxygenation of oceanic deep waters. This phenomenon suggests that Prokarya and Eukarya evolved in anoxic and oxic environments, respectively, a hypothesis further supported by structures and functions of Fe-binding proteins in each Superkingdom. Also observed is a proliferation in the diversity of Zn-binding protein structures involved in protein-DNA and protein-protein interactions within Eukarya, an event unlikely to occur in either an anoxic or euxinic environment where Zn concentrations would be vanishingly low. We hypothesize that these conserved trends are proteomic imprints of changes in trace metal bioavailability in the ancient ocean that highlight a major evolutionary shift in biological trace metal usage.

Landry, DM, Kristiansen S, Palenik BP.  2009.  Molecular characterization and antibody detection of a nitrogen-regulated cell-surface protein of the coccolithophore emiliania huxleyi (prymnesiophyceae). Journal of Phycology. 45:650-659.   10.1111/j.1529-8817.2009.00693.x   AbstractWebsite

Dissolved organic nitrogen (DON) can account for a significant portion of total nitrogen in some aquatic environments, and many species of phytoplankton are able to scavenge nitrogen from this pool especially when inorganic nitrogen is limiting. Emiliania huxleyi (Lohmann) H. W. Hay et H. Mohler is able to use various forms of DON for growth, including several amino acids, purines, and pyrimidines. A cell-surface protein up-regulated in the absence of inorganic nitrogen, NRP1, is hypothesized to play a role in the metabolism of one or more of these organic nitrogen forms. Here, the genomic and cDNA sequence of NRP1 is reported. Structural predictions based on the amino acid sequence suggest a pyridoxal-5'-phosphate-dependent enzyme that may have a role in acquiring nitrogen from amino acids. Further evidence for the function of NRP1 is measured in spent media from nitrogen-limited cultures, which contain NRP1 and have glutaminase and formamidase activity. Field studies using an antibody to NRP1 show that it is expressed in E. huxleyi during bloom conditions in a Norwegian fjord.

Landry, DM, Gaasterland T, Palenik BP.  2006.  Molecular characterization of a phosphate-regulated cell-surface protein from the coccolithophorid, Emiliania huxleyi (Prymnesiophyceae). Journal of Phycology. 42:814-821.   10.1111/j.1529-8817.2006.00247.x   AbstractWebsite

Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophorid that is known to be an excellent competitor for phosphate. A previous survey of cell-surface proteins induced by phosphorus limitation in strain CCMP 374 yielded three abundant proteins. Using CCMP 1516, the strain chosen for genome sequence determination, we report the cDNA, genomic, and amino acid sequence of one cell-surface phosphorus-limitation induced protein and evidence that a second protein is highly similar. The introns within the genomic DNA encoding this cell-surface protein as well as those defined by other phosphate-regulated expressed sequence tags are analyzed. As these proteins are the most abundant cell-surface proteins present under phosphorus limitation, they likely have a role in the ability of this organism to compete for phosphate.

Palenik, B, Wood MA.  1998.  Molecular markers of phytoplankton status and their application at the level of individual cells. Molecular Approaches To The Study Of The Ocean. ( Cooksey KL, Ed.).:187-205., New York: Chapman & Hall Abstract
Palenik, B.  2015.  Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment. Annual Review of Marine Science, Vol 7. 7:325-340.   10.1146/annurev-marine-010814-015639   AbstractWebsite

Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.

Palenik, B, Haselkorn R.  1992.  Multiple evolutionary origins of prochlorophytes, the chlorophyll b-containing prokaryotes. Nature. 355:265-267.   10.1038/355265a0   AbstractWebsite

PROCHLOROPHYTES are prokaryotes that Carry out oxygenic photosynthesis using chlorophylls a and b, but lack phycobiliproteins as light-harvesting pigments 1. These characteristics distinguish them from cyanobacteria, which contain phycobiliproteins, but no chlorophyll b. Three prochlorophyte genera have been described: Prochloron 1-3, Prochlorothrix 4 and Prochlorococcus 5,6. The prochlorophytes share their pigment characteristics with green plant and euglenoid chloroplasts, which has led to a debate on whether these chloroplasts may have arisen from an endosymbiotic prochlorophyte rather than a cyanobacterium 2,7. Molecular sequence data, including those presented here based on a fragment of the rpoC1 gene encoding a subunit of DNA-dependent RNA polymerase, indicate that the known prochlorophyte lineages do not include the direct ancestor of chloroplasts 8-11. We also show that the prochlorophytes are a highly diverged polyphyletic group. Thus the use of chlorophyll b as a light-harvesting pigment has developed independently several times in evolution. Similar conclusions have been reached in parallel studies using 16S ribosomal RNA sequences 12.