Journal Article

Microbial metalloproteomes are largely uncharacterized

Scott, Joseph W., Poole II, Farris L., Apon, Junefredo V., Jenney Jr, Francis E., Menon, Angeli Lal, Yannone, Steven M., Adams, Michael W. W., Thorgersen, Michael P., Cvetkovic, Aleksandar, Vaccaro, Brian J., Trauger, Sunia A., Siuzdak, Gary, Tainer, John A., Lancaster, W. Andrew, Praissman, Jeremy L., Shanmukh, Saratchandra, Kalisiak, Ewa

2010

Overview

Metalloprotein diversity Metalloproteins are key components in many biological processes, including respiration, photosynthesis and drug metabolism. The presence of a metal in a protein is often not apparent until the molecule is fully characterized. For this reason, and because of the diversity of metal coordination sites, it is not yet possible to use genome sequences to predict the types of metal an organism utilizes from its environment, or to determine the composition of the organism's metalloproteins. Cvetkovic et al . have therefore taken an alternative route, using conventional liquid chromatography to identify the metals in an organism — the hyperthermophilic marine archaeon Pyrococcus furiosus — and proteomics to examine the metalloproteins. Of the 343 metal peaks in chromatography fractions, 158 did not match any known or predicted metalloprotein, some of them containing metals that the organism was not previously known to utilize. This work suggests that metalloproteomes are more extensive and diverse than previously thought. Metalloproteins are important in many biological processes, including respiration, photosynthesis and drug metabolism. Using genome sequences to predict the numbers and types of metal an organism uses is currently very challenging. These authors used a proteomics approach to identify and characterize a large number of a microorganism's metalloproteins on a genome-wide scale, and successfully separated and identified its cytoplasmic metalloproteins. Metal ion cofactors afford proteins virtually unlimited catalytic potential, enable electron transfer reactions and have a great impact on protein stability 1 , 2 . Consequently, metalloproteins have key roles in most biological processes, including respiration (iron and copper), photosynthesis (manganese) and drug metabolism (iron). Yet, predicting from genome sequence the numbers and types of metal an organism assimilates from its environment or uses in its metalloproteome is currently impossible because metal coordination sites are diverse and poorly recognized 2 , 3 , 4 . We present here a robust, metal-based approach to determine all metals an organism assimilates and identify its metalloproteins on a genome-wide scale. This shifts the focus from classical protein-based purification to metal-based identification and purification by liquid chromatography, high-throughput tandem mass spectrometry (HT-MS/MS) and inductively coupled plasma mass spectrometry (ICP-MS) to characterize cytoplasmic metalloproteins from an exemplary microorganism ( Pyrococcus furiosus ). Of 343 metal peaks in chromatography fractions, 158 did not match any predicted metalloprotein. Unassigned peaks included metals known to be used (cobalt, iron, nickel, tungsten and zinc; 83 peaks) plus metals the organism was not thought to assimilate (lead, manganese, molybdenum, uranium and vanadium; 75 peaks). Purification of eight of 158 unexpected metal peaks yielded four novel nickel- and molybdenum-containing proteins, whereas four purified proteins contained sub-stoichiometric amounts of misincorporated lead and uranium. Analyses of two additional microorganisms ( Escherichia coli and Sulfolobus solfataricus ) revealed species-specific assimilation of yet more unexpected metals. Metalloproteomes are therefore much more extensive and diverse than previously recognized, and promise to provide key insights for cell biology, microbial growth and toxicity mechanisms.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/326 / 631/45 / 631/92 / 631/92/612/1141 / Bacterial proteins / Bacterial Proteins - analysis / Bacterial Proteins - chemistry / Bacteriology / BASIC BIOLOGICAL SCIENCES / biochemistry / Biological and medical sciences / chemical biology / Chromatography, Liquid / Chromosome mapping / Cobalt / DNA repair / DNA sequencing / E coli / Escherichia coli / Escherichia coli - chemistry / Fundamental and applied biological sciences. Psychology / Genomics / Humanities and Social Sciences / INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY / Iron / Lead / letter / Liquid chromatography / Manganese / Mass spectrometry / Metalloproteins / Metalloproteins - analysis / Metalloproteins - chemistry / Metals / Metals - analysis / Metals - chemistry / Metals - metabolism / Methods / Microbiology / Microorganisms / Molybdenum / multidisciplinary / Nickel / Nucleotide sequencing / Organisms / Photosynthesis / Properties / Proteins / Proteome - analysis / Proteome - chemistry / Proteomics / Purification / Pyrococcus furiosus / Pyrococcus furiosus - chemistry / Pyrococcus furiosus - metabolism / Recognition / Science / Science (multidisciplinary) / Sulfolobus solfataricus / Sulfolobus solfataricus - chemistry / Tandem Mass Spectrometry / Tungsten / Uranium / Vanadium