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Chen, X, Su Z, Dam P, Palenik B, Xu Y, Jiang T.  2004.  Operon prediction by comparative genomics: an application to the Synechococcus sp WH8102 genome. Nucleic Acids Research. 32:2147-2157.   10.1093/nar/gkh510   AbstractWebsite

We present a computational method for operon prediction based on a comparative genomics approach. A group of consecutive genes is considered as a candidate operon if both their gene sequences and functions are conserved across several phylogenetically related genomes. In addition, various supporting data for operons are also collected through the application of public domain computer programs, and used in our prediction method. These include the prediction of conserved gene functions, promoter motifs and terminators. An apparent advantage of our approach over other operon prediction methods is that it does not require many experimental data (such as gene expression data and pathway data) as input. This feature makes it applicable to many newly sequenced genomes that do not have extensive experimental information. In order to validate our prediction, we have tested the method on Escherichia coli K12, in which operon structures have been extensively studied, through a comparative analysis against Haemophilus influenzae Rd and Salmonella typhimurium LT2. Our method successfully predicted most of the 237 known operons. After this initial validation, we then applied the method to a newly sequenced and annotated microbial genome, Synechococcus sp. WH8102, through a comparative genome analysis with two other cyanobacterial genomes, Prochlorococcus marinus sp. MED4 and P.marinus sp. MIT9313. Our results are consistent with previously reported results and statistics on operons in the literature.

Chisholm, SW, Frankel SL, Goericke R, Olson RJ, Palenik B, Waterbury JB, Westjohnsrud L, Zettler ER.  1992.  Prochlorococcus marinus nov. gen. nov. sp.: An oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b . Archives of Microbiology. 157:297-300.   10.1007/bf00245165   AbstractWebsite

Several years ago, prochlorophyte picoplankton were discovered in the N. Atlantic. They have since been found to be abundant within the euphotic zone of the world's tropical and temperate oceans. The cells are extremely small, lack phycobiliproteins. and contain divinyl chlorophyll a and b as their primary photosynthetic pigments. Phylogenies constructed from DNA sequence data indicate that these cells are more closely related to a cluster of marine cyanobacteria than to their prochlorophyte 'relatives' Prochlorothrix and Prochloron. Several strains of this organism have recently been brought into culture, and herewith are given the name Prochlorococcus marinus.

Collier, JL, Palenik B.  2003.  Phycoerythrin-containing picoplankton in the Southern California Bight. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 50:2405-2422.   10.1016/s0967-0645(03)00127-9   AbstractWebsite

Flow cytometry was used to examine the distribution of phycoerythrin-rich picophytoplankton. referred to here as Synechococcus, off the Southern California coast during six California Cooperative oceanic Fisheries Investigations (CalCOFI) cruises. Depth profiles revealed that Synechococcus was most abundant in the surface mixed layer, gradually disappearing with depth below the thermocline. Within the surface mixed layer, Synechococcus abundance was generally greater and more variable at stations shoreward of the California Current than at stations offshore of it. In waters associated with the California Current not impacted by upwelling, Synechococcus abundance increased with increasing bulk chlorophyll. In contrast, Synechococcus abundance declined with increasing bulk chlorophyll at stations that were impacted by upwelling. Synechococcus at stations impacted by upwelling also had more phycoerythrin per cell than at non-upwelling stations. Offshore of the California Current, Synechococcus cells in waters intruding from the Central North Pacific displayed higher side-scatter relative to forward scatter than did Synechococcus cells elsewhere in the region. Flow cytometrically distinct Synechococcus cell types were also detected below the thermocline at most of the stations where depth profiles were analyzed. These patterns in Synechococcus abundance and cellular characteristics might reflect physiological and/or genetic differences among Synechococcus associated with the various water masses that comprise the CalCOFI region. The data presented here provide a framework from which to launch more detailed and mechanistic studies examining the role of Synechococcus in the CalCOFI ecosystem. (C) 2003 Elsevier Ltd. All rights reserved.

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.