Genetic Identification of a High-Affinity Ni Transporter and the Transcriptional Response to Ni Deprivation in Synechococcus sp. Strain WH8102

Abstract

dOne biological need for Ni in marine cyanobacteria stems from the utilization of the Ni metalloenzyme urease for the assimilation of urea as a nitrogen source. In many of the same cyanobacteria, including Synechococcus sp. strain WH8102, an additional and obligate nutrient requirement for Ni results from usage of a Ni superoxide dismutase (Ni-SOD), which is encoded by sodN. To better understand the effects of Ni deprivation on WH8102, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted. The global transcriptional response to Ni deprivation depends upon the nitrogen source provided for growth; fewer than 1% of differentially expressed genes for Ni deprivation on ammonium or urea were concordantly expressed. Surprisingly, genes for putative Ni transporters, including one colocalized on the genome with sodN, sodT, were not induced despite an increase in Ni transport. Knockouts of the putative Ni transporter gene sodT appeared to be lethal in WH8102, so the genes for sodT and sodN in WH8102 were interrupted with the gene for Fe-SOD, sodB, and its promoter from Synechococcus sp. strain WH7803. The sodT::sodB exconjugants were unable to grow at low Ni concentrations, confirming that SodT is a Ni transporter. The sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type, presumably due to a relaxed competition between urease and Ni-SOD for Ni. Both sodT::sodB and sodN::sodB lines exhibited an impaired ability to grow at low Fe concentrations. We propose a posttranslational allosteric SodT regulation involving the binding of Ni to a histidine-rich intracellular protein loop.

Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species

“…Comparing the results of this study to previous microarray experiments on the response of marine Synechococcus to nutrient limitation [phosphate starvation (Tetu et al, 2009), (Ostrowski et al, 2010)] heavy metal stress [copper toxicity (Stuart et al, 2009)] and nickel starvation (Dupont et al, 2012), it appears that the transcriptional response to different “types” of stress tend to be quite specific and can differ substantially between strains. In each study the set of genes showing the highest transcriptional increase differed.…”

“…The large number of datasets concerning transcriptional responses of WH8102 to a range of stress conditions [copper toxicity (Stuart et al, 2009), phosphate starvation (Tetu et al, 2009) and nickel starvation (Dupont et al, 2012)] enabled us to conduct cluster analyses which revealed a cluster of stress related genes upregulated in most treatments (Figure 2). This set of upregulated genes encodes functions such as Clp endopeptidase, heat shock proteins, chaperones and cell division proteins.…”

“…WH8102 genes whose expression was affected similarly by growth under a large number of stress conditions. The expression levels for this strain under eight different stress conditions: early and late phosphate stress (Tetu et al, 2009), EB and MC shock (this study), moderate and high copper shock (pCu11; pCU10) (Stuart et al, 2009) and Nickel (Ni) deprivation in cultures growing on NH4 + and urea (Dupont et al, 2012) were compared. For each set of experiments data from two independent biological replicates was used.…”

Trace elements at the intersection of marine biological and geochemical evolution

“…Several recent molecular innovations are employed by organisms in the modern environment to reduce Fe requirements-but always with a tradeoff. These tradeoffs include; the replacement of a Fe-containing superoxide dismutase with a Nicontaining version (Dupont et al, 2012), exchanging an Fe protein with a Cu protein in the electron transport chains in photosynthesis (Peers and Price, 2006) and ammonia oxidation (Santoro et al, 2015), and using B 12 instead of Fe for ribonucleotide reductase.…”

Gene annotation and functional analysis of a newly sequenced Synechococcus strain

“…In another study, the genome-wide metabolic network of S. elongatus PCC 7942 was reconstructed by metabolic flux simulation models, and the applicability of the model was demonstrated by simulating the autotrophic growth conditions of this strain (Triana et al, 2014). Comparatively, parallel microarray-based analysis of gene expression and gene knockout experiments were conducted for Synechococcus sp WH 8102, and the results showed that the sodT::sodB exconjugants were unable to grow at low Ni concentrations while the sodN::sodB exconjugants displayed higher growth rates at low Ni concentrations than did the wild type (Dupont et al, 2012).The genome sizes of the common Synechococcus strains are less than 3Mb and the numbers of genes are less than 3000. However, the genome of the newly sequenced strain S.PCC7336 is over 5Mb, and is therefore likely to carry unique structures and functional genes.…”