Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ~40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0452883)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0752291)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0723667)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0928414)National Science Foundation (U.S.). Polar Program (ANT-0732665)United States. Environmental Protection Agency (Star Fellowship)Woods Hole Oceanographic Institution. Ocean Life InstituteCenter for Microbial Oceanography: Research and EducationCenter for Environmental Bioinorganic Chemistr

The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito

Examination of Microbial Proteome Preservation Techniques Applicable to Autonomous Environmental Sample Collection

Improvements in temporal and spatial sampling frequency have the potential to open new windows into the understanding of marine microbial dynamics. In recent years, efforts have been made to allow automated samplers to collect microbial biomass for DNA/RNA analyses from moored observatories and autonomous underwater vehicles. Measurements of microbial proteins are also of significant interest given their biogeochemical importance as enzymes that catalyze reactions and transporters that interface with the environment. We examined the influence of five preservatives solutions (SDS-extraction buffer, ethanol, trichloroacetic acid, B-PER, and RNAlater) on the proteome integrity of the marine cyanobacterium Synechococcus WH8102 after four weeks of storage at room temperature. Four approaches were used to assess degradation: total protein recovery, band integrity on an SDS-PAGE gel, and number of protein identifications and relative abundances by 1D LC-MS/MS proteomic analyses. Total protein recoveries from the preserved samples were lower than the frozen control due to processing losses, which could be corrected for with internal standardization. The trichloroacetic acid preserved sample showed significant loss of protein band integrity on the SDS-PAGE gel. The RNAlater preserved sample showed the highest number of protein identifications (103% relative to the control; 520 + 31 identifications in RNAlater versus 504 + 4 in the control), equivalent to the frozen control. Relative abundances of individual proteins in the RNAlater treatment were quite similar to that of the frozen control (average ratio of 1.01 + 0.27 for the 50 most abundant proteins), while the SDS-extraction buffer, ethanol, and B-PER all showed significant decreases in both number of identifications and relative abundances of individual proteins. Based on these findings, RNAlater was an effective proteome preservative, although further study is warranted on additional marine microbes

Health science community will miss this bright and uniting star : in memory of Professor Gjumrakch Aliev, M.D, Ph.D

No abstract availablehttp://www.mdpi.com/journal/cancerspm2021Physiolog

Transcript, protein, and physiological parameters linked to phosphorus deficiency.

<p>Normalized transcript and protein abundance for significantly differentially regulated signatures and their associated physiological patterns, for polyphosphate metabolism (A), phosphate transport (B), alkaline phosphatase (C, D), phosphodiesterase (E), and sulfolipid synthesis (F) across P-replete (+P) and P-deficient (-P) conditions. Protein data are distinguished with a “p” next to the PID and by the hatched pattern. Polyphosphate abundances as measured by solid state ³¹P NMR (A) and enzyme activities (C, E), were assayed and are reported below each graph. Cell-associated alkaline phosphatase activity (green color) was detected using an enzyme labeled fluorescence substrate. The green fluorescence indicating enzyme activity is present in -P cells (panels 1, 2, 4, 5, and 6) and not present in +P cells (panel 3) (D). Chlorophyll autofluorescence (red) in also visible. Panels 4, 5, and 6 are a Z series through a labeled –P cell. The SQDG:PC ratio is reported from Van Mooy et al. (2009) from replete and P-deficient <i>T. pseudonana</i> cultures <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033768#pone.0033768-VanMooy1" target="_blank">[51]</a>, which were grown similarly to those in this study. SQDG: sulphoquinovosyldiacylglyerol; PG: phosphatidylglycerol.</p

Comparison of transcript and protein signals.

<p>Comparison of proteome and transcriptome changes in response to P deficiency. Fold-change presented as the log₂ of the ratio of deficient∶replete conditions. Unity lines are shown in grey solid (fold-change = 1), while a linear regression (log₂[proteins] = 0.49*log₂[transcripts]-0.25) of proteins that are >2-fold in abundance in either treatment against their corresponding transcripts is shown in yellow (r² = 0.53). The dashed line is the 1∶1 line denoting equal fold change between the deficient and replete conditions for the transcriptome and the proteome. Proteins and transcripts of interest that correspond to P-metabolism, glycolysis and ribosomes/translation are highlighted.</p