A Soluble 3D LC/MS/MS Proteome of the Filamentous Cyanobacterium Nostoc punctiforme D. C. Anderson,*,† Elsie L. Campbell,‡ and John C. Meeks‡ Institute of Molecular Biology, University of Oregon, Eugene Oregon 97403, and Section of Microbiology, University of California, Davis, California 95616 Received June 5, 2006
Nostoc punctiforme is an oxygenic photoautotrophic cyanobacterium with multiple developmental states, which can form nitrogen-fixing symbioses with a variety of terrestrial plants. 3D LC/MS/MS shotgun peptide sequencing was used to analyze the proteome when N. punctiforme is grown in continuous moderate light with ammonia as the nitrogen source. The soluble proteome includes 1575 proteins, 50% of which can be assigned to core metabolic and transport functions. Another 39% are assigned to proteins with no known function, a substantially higher fraction than in the Escherichia coli proteome. Many expressed proteins protect against oxidative and light stress. Seventy-one sensor histidine kinases, response regulators, and serine/threonine kinases, individually and as hybrid, multidomain proteins, were identified, reflecting a substantial capacity to sense and respond to environmental change. Proteins encoded by each of the five N. punctiforme plasmids were identified, as were 10 transposases, reflecting the plasticity of the N. punctiforme genome. This core proteome sets the stage for comparison with that of other developmental states. Keywords: Cyanobacteria • Nostoc punctiforme • proteome analysis • shotgun peptide sequencing • systems biology
Introduction Cyanobacteria are a phylogenetically cohesive and ancient prokaryotic lineage, with a chemical and morphological fossil record extending to about 3 billion years ago.1 The unifying characteristic of cyanobacteria is oxygen-evolving photosynthesis, which was responsible for the production of excess oxygen on earth.2 Morphological and developmental differences, such as unicellular or filamentous growth, plane of cell division, and formation of specialized cells appear to have diverged early in cyanobacterial evolution.3 The filamentous cyanobacterium Nostoc punctiforme is unique in expressing multiple vegetative developmental alternatives, and in fixing nitrogen in both free-living and symbiotic growth states.4 Nitrogen fixation is not compatible with oxygenevolving photosynthesis due to the oxygen lability of the nitrogenase enzyme complex.5 Some cyanobacteria, such as Anabaena and Nostoc, have solved this problem by confining nitrogenase expression to specialized cells called heterocysts. Heterocysts lack oxygen-evolving photosynthesis, have an increased rate of aerobic respiration, and synthesize a solute and gas-impermeable extra wall layer, all of which contribute to low cytoplasmic levels of oxygen.6 N. punctiforme establishes symbioses with representatives of three of the major groups of terrestrial plants: bryophyte hornworts and liverworts, gymnosperm cycads, and the angiosperm Gunnera.7 In these * To whom correspondence should be addressed. E-mail: dca0204@ molbio.uoregon.edu. † University of Oregon. ‡ University of California.
3096
Journal of Proteome Research 2006, 5, 3096-3104
Published on Web 09/28/2006
symbioses, the frequency of heterocyst differentiation and nitrogen fixation increase 3- to 5-fold, and fixed nitrogen as ammonium is made available to the plant partner. Establishment of a symbiotic association requires the differentiation by N. punctiforme of motile filaments called hormogonia. The differentiation and behavior of hormogonia are influenced by chemical signals from the plant partner.8 Under unfavorable growth conditions, in the presence or absence of a plant partner, N. punctiforme differentiates spore-like cells called akinetes. N. punctiforme also expresses a number of physiological adaptations to changing growth environments, such as respiratory heterotrophic growth, alteration of light harvesting complexes in response to light quality and quantity, production of UV-light absorbing compounds, and production of secondary metabolites such as cyclic substituted peptides.9 The N. punctiforme strain ATCC 29133 genome has been completely sequenced and is large for a prokaryote, encoding 7465 genes, which includes 7364 putative proteins and 101 stable RNA species (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi). The genome is contained on an 8.23 Mbp circular chromosome and five plasmids of 26, 65.9, 123, 254.9, and 354.5 kbp, respectively. The size of the genome is consistent with the complex phenotypic traits and life style expressed by N. punctiforme, but its annotation does not identify the regulatory and metabolic pathways characteristic of the various traits. Only a subset of the genome may be expressed under the different growth and environmental stress conditions that N. punctiforme may encounter. We are approaching functional genome analysis by defining the proteome in specifically 10.1021/pr060272m CCC: $33.50
2006 American Chemical Society
research articles
Soluble 3D LC/MS/MS Proteome
cultured steady state and transitional cultures. Functional genome information will form a foundation for the potential engineering of N. punctiforme and related organisms for specific purposes, such as bioreactor-based photosynthetic hydrogen, ammonium, or other metabolite production. A preliminary proteome, using 2D gels and LC/MS/MS analysis of in-gel digests, identified 49 N. punctiforme proteins.10 Here we report the first large scale analysis of the expressed N. punctiforme proteome by identifying 1574 proteins in the soluble fraction of an ammonium-grown culture. We use gel filtration to first separate the soluble proteins and then 2D LC/MS/MS shotgun peptide sequencing of the tryptic peptides taken from each molecular sizing fraction for protein identification. We used culture in continuous moderate light with ammonium as the nitrogen source, as this is the most permissive growth condition for N. punctiforme, in which only physiologically identical vegetative cells are present. This culture state should thus yield the minimal proteome to which comparisons of developmental and symbiotic cultures can be made.
Experimental Section Culture and Lysis of N. punctiforme. N. punctiforme was cultured in a minimal salts medium,11 diluted 4-fold, supplemented with 2.5 mM NH4Cl, and buffered with 5.0 mM Mops, pH 7.8. The culture volume was 500 mL in a 1 L flask, placed in an incubator-shaker operating at 260 rpm and 24 °C, with coolwhite fluorescent light of 70 µmol/m2/s. The cells were harvested by 5 min centrifugation at 1000g and room temperature, suspended in lysis buffer, and lysed by passage through a French pressure cell. The lysis buffer was 750 mM phosphate, pH 8.0, supplemented with protease inhibitor cocktail 1 (SigmaAldrich) at 1 mL/20 g of cell pellet. The lysate was centrifuged at 150000g and 4 °C for 2 h and the supernatant (water soluble) fraction retained for analysis. Protein Fractionation and 2D Capillary LC/MS/MS Analysis. A volume containing 450 µg soluble protein was loaded onto a 1 × 21 cm Sephacryl S-400 column equilibrated in 0.1 M Tris buffer, pH 8.5 with 0.1 M NaCl. The column was eluted on an Agilent 1100 HPLC at 100 µL/min and fractions were collected every 5 min, starting 45 min into the run. Twentyeight fractions were individually subjected to a 20 min denaturation at 90 °C in 8 M urea, with 20 mM methylamine added to prevent lysine carbamylation, reduction with 10 mM dithiothreitol, and alkylation with 30 mM iodoacetamide, followed by digestion with trypsin (1 µg per 25 µg protein). The trypsin digested individual fractions were vacuum centrifuged to less than 1 mL, formic acid was added to ∼1% v/v, and the peptide mixtures were individually loaded on a Vydac C18 analytical cartridge for desalting. After the urea and salts in the above tryptic digest buffer were eluted as determined by monitoring at 206 nm, peptides were step eluted with 85% acetonitrile-0.1% formic acid and concentrated to a small volume by vacuum centrifugation. Picofrit 75 µm internal diameter capillary columns were slurry packed, sequentially, with 6-10 cm of C18 reversed phase Denali resin (Grace-Vydac Inc., Hesperia, CA) and 4-5 cm of strong cation-exchange resin (Luna 5 µm 100 A resin; Phenomenex, Torrance, CA) using a helium high-pressure chamber.12 The columns were eluted at 300 nL/min with an Agilent 1100 Nano-HPLC. Salt steps used 8 µL of pH 3.0 ammonium acetate ranging from 10 mM to 2.0 M and a final injection of 100% acetonitrile-0.1% formic acid to clean sticky peptides from the C18 resin. The reversed phase
dimension was eluted with a gradient from 5 to 85% acetonitrile at 1%/min and injected into the MS via a New Objective electrospray source. Overall, data from 8 to 10 individual salt steps and washes were collected for each gel filtration column fraction. Two-dimensional (2D) LC/MS/MS data were collected on a ThermoFinnigan LCQ Deca XP Plus 3D ion trap, using one full scan from 350 to 1800 m/z followed by 5 MS/MS scans at 35% relative collision energy. Proteins were analyzed using SEQUEST v. 27,13,14 allowing for cysteine alkylation with iodoacetamide and methionine oxidation, and with 1.5 and 1 Da precursor and fragment ion tolerances, respectively. DTA files for both +2 and +3 charge states were generated and searched. Strict trypsin specificity was required15 and a maximum of two missed cleavage sites was allowed in a tryptic peptide. Peptides were analyzed using the support vector machine learning algorithm GIST,16 an automated implementation of which was integrated into the software suite MASSIEVE. A 13 parameter training set for the N. punctiforme proteome was constructed by adding the sequences of known proteins into the N. punctiforme protein sequence database and analyzing 2D-LC/ MS/MS/Sequest data for whole test protein tryptic peptide maps using GIST.16 Proteins were considered identified if they had at least one peptide meeting filtering criteria of Washburn et al.,17 i.e., a delta Cn of 0.08 or higher and an Xcorr of 1.9 for +1 ions, 2.2 for +2 ions or 3.7 for +3 ions, or at least one peptide with a support vector machine analysis-derived probability of a least 90% of being correctly sequenced16 (Supplementary Table 1 in Supporting Information). The probability of correct sequencing of a peptide was derived by fitting the discriminant values produced by the support vector machine to a sigmoid function18 (see http://microarray.cpmc.columbia.edu/gist/fit-sigmoid.html). In calculating the number of different peptides identifying a protein, peptides with modified residues are included since they are fragmented and sequenced independently. N. punctiforme Gene Sequences. The sequences of N. punctiforme genes/proteins used in the SEQUEST database searches were obtained from http://genome.ornl.gov/microbial.npun and were from the 22 December 2003 annotated version of the genome. These sequences were produced by the US Department of Energy Joint Genome Institute and may also be accessed from the Integrated Microbial Genomes site (http://img.jgi.doe.gov/ cgi-bin/pub/main.cgi). The functional category of each protein was initially based on COG functional group analysis by the ORNL Computational Biology Group (http://genome.ornl.gov/microbial.npun/22dec03/fun.html). All protein identities were then manually curated (Supplementary Table 2 in Supporting Information).
Results and Discussion Isolating the Proteome. The proteome was first fractionated at the protein level by gel filtration to extend the dynamic range of protein identification and to reduce the complexity of peptides analyzed in each fraction after tryptic digestions. The gel filtration chromatogram for the isolation of the N. punctiforme soluble proteome is shown in Figure 1. Twenty-eight fractions (fraction in inset of Figure 1) were collected starting at 45 min into the elution and analyzed by capillary 2D strong cation exchange/reversed phase LC/MS/MS. The total number of proteins identified in each fraction are listed in the insert for Figure 1 (prot). These proteins were identified using a twoparameter filtration (Xcorr and delta Cn17). Additional proteins Journal of Proteome Research • Vol. 5, No. 11, 2006 3097
research articles
Anderson et al.
Figure 1. Gel filtration of the soluble Nostoc punctiforme proteome. About 450 µg of soluble N. punctiforme protein was gel filtered on a Sephacryl S400 column. Five minute fractions were collected starting at 45 min. Proteins in each of the 28 fractions collected were digested with trypsin, and the peptides were sequenced by capillary 2D LC/MS/MS. The total proteins identified in each fraction are listed in the inset (prot). Proteins not identified by two-parameter filters but identified by at least one peptide with a 90% probability of correct sequencing, derived from support vector machine learning analysis, are listed in the 90% column. Overall, 1575 proteins were identified.
with at least one peptide with a 90% probability of correct sequencing, which were identified by machine learning analysis and not by the filters, are also included. Proteins were identified in every fraction examined. Except for the first three and the last fractions, the identified proteins were roughly evenly divided between individual fractions, illustrating the utility of separate protein and peptide columns for fractionation of a large number of proteins. Overall, 1574 unique proteins were identified. The sum of the identified proteins in the 28 fractions is 5463, evidence of an average 3.5fold redundancy of protein identification. Use of machine learning analysis for protein identification increased overall coverage by about 100 proteins. The number of identified proteins in each fraction was more evenly distributed than the marked A280 nm peak in fractions 18-19, suggesting the possibility that molecules other than proteins in the lysate supernatant may have contributed to the overall A280 nm profile, consistent with the loading of the entire lysate supernatant (proteins and other molecules) onto the gel filtration column. Fractions were collected starting at the void volume of the gel filtration column, and continued until well after the elution position of a low molecular weight standard, to account for 3098
Journal of Proteome Research • Vol. 5, No. 11, 2006
the possibility that some proteins might stick to the resin and elute later than expected based on their molecular size. However, it is possible that some low molecular mass proteins, or very sticky proteins, were lost in fractions eluting after 190 min. Identified Proteome. The identified proteins were grouped into five categories with respect to their predicted functional role in the physiology of N. punctiforme (Table 1 and Supplementary Table 2) or any bacterium.19 i. Core metabolic proteins are those involved in synthesis of the 12 precursor sugar or acid molecules (i.e. ribose-5-phosphate, 2-oxoglutarate), conversion of precursors to monomers (amino acids, nucleotides and nucleosides, fatty acids and elemental components), and polymerization of monomers into proteins, DNA, RNA, lipids, peptidoglycan, and porphyrins (pigments and heme proteins). Included in the polymer-forming proteins are those involved in protein processing and turnover, DNA repair, DNA and RNA modification, and synthesis of the cell envelope. Also included in core function are proteins for cell division and chromosome segregation, storage of metabolites, and metabolism of reactive oxygen species and toxic metabolites (assignment of the latter proteins to the core category will be elaborated below). ii.
research articles
Soluble 3D LC/MS/MS Proteome Table 1. Summary of the Functional Categories Assigned to the N. punctiforme Proteome i. Core Metabolism, 719 Proteins, 46%
no.
precursors cofactors energy monomers amino acids fatty acids nucleic acids elemental components polymers protein synthesis protein processing-chaperones protein turnover DNA metabolism RNA metabolism Lipid metabolism cell envelope porphyrins cell division storage metabolic protection reactive oxygen species methylglyoxal
74 49 28 132 73 12 33 14 364 96 52 33 47 20 9 73 34 17 21 34 29 5
iv. Selfish Metabolism, 13 Proteins, 1% phage transposases
3 10
Transport proteins are involved in both acquisition of nutrients and export or secretion of peptides and metabolites. These may be considered as core metabolic proteins, but they readily cluster in bioinformatics analyses and were analyzed as a unit. iii. Adaptive metabolic proteins are those involved in signal transduction pathways (including stress responses), transcriptional regulation, growth on alternative nitrogen or phosphate sources, synthesis of secondary metabolites, and regulation of cellular development alternatives. iv. The selfish metabolic category includes transposases and phage specific proteins. v. Unassigned proteins include those that contain distinct domains or motifs (i.e. ATP binding) but have an unassigned cellular function, as well as conserved hypothetical proteins and hypothetical proteins unique to N. punctiforme. Proteins in this category have no known function. i. Core Metabolic Proteins. The largest category of proteins identified (719) was that of core metabolic functions, which constituted 46% of the soluble proteome (Table 1). A similar categorization of the N. punctiforme annotated genes implies about 23% of the genome (1675 genes) could be involved in core metabolism.20 As would be predicted from traditional physiological and biochemical databases, core metabolic proteins are disproportionately represented in the permissivegrowth proteome compared to the genome, although less than half of the potential putative gene products could be detected. Most of these proteins are involved in precursor, monomer, and especially polymer synthesis, including a substantial investment of 73 proteins for synthesis of the cell envelope. Wellknown metabolic pathways, such as for amino acid (73 proteins), nucleic acid (33 proteins), cofactor (49 proteins), and protein (96 proteins) synthesis, can be reconstructed from the proteome. Cyanobacteria assimilate carbon dioxide into sugar via the reductive pentose phosphate pathway (Calvin-Benson-Bassham cycle) and catabolize hexoses via the oxidative pentose phosphate pathway. Reductive and oxidative pentose phosphate metabolism can also be reconstructed from the proteome, including several proteins of redundant predicted function (three glucose-6-phosphate dehydrogenases, two 6-phos-
ii. Transport Metabolism, 69 Proteins, 4%
import permeases and ion transporters ATP binding periplasmic binding porters-channels regulatory proteins export iii. Adaptive Metabolism, 166 Proteins, 11% signal transduction histidine kinase HK + response regulator HK + protein kinase response regulator protein kinase protein kinase phosphatase global signal stress taxis transcriptional regulation secondary metabolism alternative nitrogen-phosphate development v. Unassigned Metabolism, 608 Proteins, 39% conserved hypothetical hypothetical unassigned
no.
50 21 6 18 3 2 19 98 35 5 4 20 7 3 16 6 3 24 28 10 5 327 62 225
phogluconate dehydrogenases, three transaldolases, and two transketolases). The presence of three putative glucose 6-phosphate dehydrogenase proteins is striking because mutation of one (NpF4025) leads to defective phenotypes in nitrogen fixation and dark growth.21 Thus, the role of the alternative enzymes is not clear. A similar redundancy can be seen in the cluster of 52 proteins for protein processing, which contains six distinct peptidyl-prolyl cis-trans isomerases and eight Clp processing proteases. It also contains five thioredoxins, one ferredoxindependent thioredoxin reductase, and one NAD(P)H-dependent thioredoxin reductase. N. punctiforme has a significant investment of 34 proteins for the synthesis of porphyrins, leading to heme, chlorophyll a, and phycobiliproteins, the major photosynthetic light harvesting pigments. Under continuous light and nutrient replete conditions, cyanobacteria store carbon as sucrose, trehalose, and glycogen, nitrogen as cyanophycin, a unique polymer of an arginine backbone and aspartate side chains, and phosphate as polyphosphate. Present are 21 proteins for the synthesis or degradation of these polymers. The fact that these predicted proteins are present gives confidence in the robust coverage of the analysis. The top scoring 40 proteins are also overwhelmingly (85%) associated with core metabolism (Table 2). To examine the top scoring proteins, we sorted the proteome by the summed machine learning-based probabilities of the peptides identifying a protein, and selected the top 40 proteins with the highest values. For all proteins but one in Table 2, the probability of the best peptide identifying that protein was 1.0; for NpF3882, this was 0.99. The proteins are listed in descending order of the number of unique peptides identifying each protein. These should be abundant proteins. Polymer metabolism represents 45% of the abundant proteins, with the majority involved in protein synthesis (including the beta′ and gamma subunits of DNA-dependent RNA polymerase) or protein processing (including two different peptidylproyl cis-trans isomerases, plus DnaK and GrpE). Precursor metabolism, primarily as glycolytic enzymes, contributed to 18% of the abundant proteins. No hypothetical proteins are present in the abundant class, but Journal of Proteome Research • Vol. 5, No. 11, 2006 3099
research articles
Anderson et al.
Table 2. Identity of the 40 Top Scoring Proteins in the Soluble Proteome of N. punctiforme protein
number of peptides
summed peptide probabilitya
function
NpR5987 NpF3884 NpF3883 NpF4987 NpR4557 NpF4294 NpF5938 NpR3625 NpR5160 NpF0567 NpR5218 NpF3786 NpR0444 NpR0971 NpF5584 NpF0849 NpF4986 NpF1821 NpR2542 NpF3458 NpR5915 NpF0818 NpR1884 NpF5778 NpR3857 NpF6082 NpR3258 NpR6491 NpF0436 NpR5588 NpF4157 NpR4933 NpR2469 NpR6087 NpF2553 NpF0121 NpR5769 NpR3508 NpF3882 NpR5587
154 141 140 113 112 93 81 71 70 70 65 60 59 58 57 50 47 47 46 46 44 40 39 38 38 34 34 33 33 31 30 30 28 26 25 24 22 21 21 20
7.02 14.35 6.2 8.14 12.67 7.83 13.36 7.98 9.49 8.09 5.82 14.67 5.23 11.08 9.43 9.86 7.08 5.12 6.78 6.23 9.72 5.4 7.47 5.69 5.14 7.9 5.45 8.76 5.16 5.41 6.33 6.25 5.47 5.48 7.85 7.39 5.42 7.72 5.85 5.06
CORE polymer - prot process. ATPases with chaperone activity, ClpA/B CORE polymer - prot syn. Translation elongation factor Tu domain, TufA CORE polymer - prot syn. Translation elongation factor G, FusA CORE polymer - prot syn. DNA-directed RNA polymerase, beta subunit, RpoC2 CORE precursor. Transketolase, TktA CORE precursor. Carbonic anhydrase/CO2 concentrating protein, CcmM CORE precursor. Phosphoglycerate kinase, Pgk CORE polymer - RNA. Polyribonucleotide nucleotidyltransferase, Pnp CORE polymer - cell env. UDP-glucose dehydrogenase: alcohol oxidation, Ugd CORE polymer - prot process. HSP70 protein folding chaperone, DnaK CORE mono-AA. D-3-phosphoglycerate dehydrogenase. pgdh UNASSIGNED. Conserved hypothetical 4 TMb CORE precursor. Glyceraldehyde-3-phosphate dehydrogenase, Gapdh UNASSIGNED. Cation binding HHE CORE precursor. Fructose bisphosphate aldolase, CbbA CORE polymer - prot process.Trigger factor peptidyl-prolyl cis-trans isomerase, Tig CORE polymer - prot syn. DNA-directed RNA polymerase, gamma subunit, RpoC1 CORE storage - NcphB Cyanophycinase and related exopeptidases CORE polymer - porphyrin. Uroporphyrinogen-III decarboxylase, HemE CORE polymer - prot syn. Aspartyl tRNA synthetase, AspS CORE ROS. Fe-dependent peroxidase, Dyp-type CORE monomer - ion. Sulfite reductase beta subunit (hemoprotein), CysI UNASSIGNED. Conserved hypothetical UNASSIGNED. PT repeat (various weak assignments) signal P 1 TM UNASSIGNED. Conserved hypothetical. pfam ) Tic22-like signal P 1 TM CORE ROS. Peroxiredoxin, AhpC CORE ROS. DNA-binding ferritin-like protein (oxidative damage protectant) CORE ROS. Fe/Mn superoxide dismutase, SodA CORE polymer - prot syn. Prolyl-tRNA synthetase, ProS CORE monomer - nuc IMP dehydrogenase CORE monomer - AA. Serine-pyruvate aminotransferase class V CORE polymer- prot process. Cyclophilin peptidylprolyl cis-trans isomerase, PpiB CORE polymer - prot syn. Ribosomal protein S1, RpsA CORE storage - C. ADP-glucose pyrophosphorylase, GlgC CORE monomer - ion. Inorganic pyrophosphatase, Ppa CORE polymer - prot process. chaperone/HSP-70 cofactor, GrpE UNASSIGNED - some S-layer homology CORE precursor. Enolase, Eno CORE polymer - prot syn. Ribosomal protein S7, RpsG CORE polymerprot process. Thioredoxin domain-containing protein, TrxA
a Summed peptide probability refers to the sum of the individual probabilities of correct sequencing of each different peptide sequence identifying the protein. b TM, predicted transmembrane segment.
three conserved hypothetical proteins and three proteins with functional domains, but an unknown physiological role, were present. Unassigned NpR0971, with a HHE cation binding domain, could be involved in oxygen (core) or nitric oxide (adaptive) binding. Present in the proteome, but not represented in the top 40 scoring category, are proteins from two highly abundant multiprotein complexes: phycobiliproteins associated with phycobilisomes and ribulose bisphosphate carboxylase/oxygenase present in carboxysomes. Moreover, only two ribosomal proteins were in the top 40 category. Phycobiliproteins, in particular, may constitute up to 50% of the total cellular protein of a cyanobacterium,22 and, thus, should have been the most abundant proteins detected in the soluble cell extract. On the basis of the visual color of the pellet and supernatant fractions, we suggest that our relatively gentle lysis protocol in high (750 mM) osmolarity maintained the multimeric organization of phycobilisomes and, perhaps, carboxysomes and polysomes, and they largely sedimented during the centrifugal clarification. This depletion of highly abundant protein complexes may have had a beneficial effect in the 3D-LC/MS/MS analysis, analogous to depletion of highly abundant proteins in serum biomarker analysis, that subsequently allowed us to identify more of the less abundant cellular proteins. 3100
Journal of Proteome Research • Vol. 5, No. 11, 2006
N. punctiforme lives in an environment characterized by intense UV radiation in the presence of self-produced oxygen. Interestingly, four of the abundant proteins are involved in protection against oxidative stress: superoxide dismutase, peroxidase, peroxiredoxin, and a DNA-binding ferritin-like protein. In all, 34 proteins that may have a role in oxidative stress and reactive metabolite metabolism were detected in the soluble proteome (Table 3). The tripeptide glutathione is a major aqueous phase antioxidant and cofactor for antioxidant enzymes.23,24 Thus, we clustered the enzymes of glutathione metabolism in the core group, rather than in adaptive metabolism. Thioredoxins and their metabolic enzymes are categorized as core protein processing factors due to their role in conformational changes through direct reduction of disulfide bridges, or oxidation of spatially adjacent SH groups, leading to activation or inactivation of catalytic activity. Protein targets of reduction by thioredoxins and glutathione may subsequently be involved in stress metabolism, e.g. peroxiredoxins and glyoxalases. What is most striking about the proteins used for protection against oxidative stress is their redundancy. All three superoxide dismutases encoded in the genome are present in the minimal proteome. These proteins reduce superoxide radicals to hydrogen peroxide. Four catalases, including a nonheme Mn-containing homologue, five peroxiredoxins, and the
research articles
Soluble 3D LC/MS/MS Proteome Table 3. Proteins Involved in Metabolic Protection: Oxidative and Metabolic Stress gene
number of peptides
NpR6491 NpF1605 NpF5478 NpF5237 NpF3488 NpR5468 NpR4582 NpR5915 NpF6082 NpF6498 NpR0493 NpF2872 NpR4657
33 6 4 6 5 1 7 44 34 13 8 6 11
NpF4802 NpR3909 NpF2660 NpF4803 NpF0920 NpR0901 NpR4093 NpF4735 NpF6084 pNPAR176 NpF4735 NpF3258 NpR5701 NpF6212 NpF3730 NpR1005 NpF1117 NpR6391 NpR2128
1 3 6 5 6 4 9 3 2 2 1 15 9 ? 5 ? 13 7 1
NpF0268
5
NpF0942
2
protein identity
superoxide dismutase, SodA superoxide dismutase, SodB superoxide dismutase, SodB catalase, KatE catalase, KatE catalase, KatE catalase, MnCat peroxidase, Dyp-type peroxiredoxin, AphC/TSA peroxiredoxin, AphC/TSA peroxiredoxin, AphC/TSA peroxiredoxin, AphC/TSA or Q peroxiredoxin 2, AphC/TSA with glutaredoxin glutaredoxin, GrxC glutaredoxin-related gamma-glutamyltransferase, Ggt glutathione synthetase, GshS glutathione reductase, GR glutathione reductase, GR glutathione S-transferase, Gst glutathione S-transferase, Gst glutathione S-transferase, Gst glutathione S-transferase, Gst glutathione S-transferase, Gst DNA-binding ferritin-like, Dps DNA-binding ferritin-like, Dps DNA-binding ferritin-like, Dps DNA-binding ferritin-like, Dps oxygen-binding globin methylglyoxal synthase, Mgs glyoxalase I, dioxygenase domain, GlxI glyoxalase/bleomycin resistance/ dioxygenase domain, GlxI glyoxalase/bleomycin resistance/ dioxygenase domain, GlxI metal-dependent hydrolases of the glyoxalase II family, GlxII
abundant peroxidase, are present to metabolize peroxides. Five glutathione S-transferases, two glutathione reductases, and four DNA binding ferritin-like proteins are present as well. In addition, four enzymes are present to metabolize toxic methylglyoxal, formed from triosephosphate by methylglyoxal synthase. Also present in the core proteome are two DNA repair photolyases, one of which is plasmid encoded. With respect to the oxygen-producing, photosynthetic life style of N. punctiforme, we suggest that it is constantly poised to enter oxidative and light stress states. The redundancy in oxidative stress and DNA photorepair proteins, and their presence in the minimal proteome, is related to preventing entrance into such stress states, whereas in other nonphototrophic organisms the presence and concentration of families of these proteins may vary in response to the environment. Energy metabolic proteins are presumably a small fraction of the identified proteome because many are integral membrane proteins and absent in the soluble fraction. Nevertheless, some proteins of the unique and combined portions of the photosynthetic and respiratory electron transport chains were detected. Lacking are complete photosynthetic reaction centers, NADH dehydrogenase complexes, cytochrome oxidases, and ATP synthases. However, it should be noted that in all, 80 proteins were detected that contain 1 to 12 transmembrane domains, including 1 with 16 such domains.
ii. Transport Metabolic Proteins. Transport proteins contributed to 4% of the proteome (Table 1). If transport proteins are also considered as a part of core function, then 50% of the soluble proteome is known to be required for the synthesis of two cells from one. Roughly one-third of the identified transport proteins have transmembrane domains and function as permeases, channels, or porters. More soluble periplasmic solute binding proteins (18), which most often function with ABC transporters, were detected than the number of corresponding transporters (6 ATP binding domains). This bias most likely resulted from the lack of recovery of the cognate transporters, rather than a few transporters interacting with multiple periplasmic binding proteins. Nearly one-third (19) of the transport proteins are involved in export, five of which are putatively multidrug exporters, four for antimicrobial peptides, and three for hemolysin-related molecules. The exact nature of the substrates exported by these systems is unknown. iii. Adaptive Metabolic Proteins. Adaptive metabolism constituted 11% of the detectable proteome (166 proteins), with more than one-half (59%) assigned to signal transduction (Table 1). Most of these proteins are likely present constitutively to sense changes in the environment and immediately initiate a physiological response by altering the cellular protein composition or protein activity. Almost 18% (1282 genes) of the N. punctiforme genome is predicted to be involved in adaptive metabolism. However, adaptive proteins, especially those of signal transduction, tend to be present in relatively low concentrations and difficult to detect in the proteome. This observation presumably accounts for the absence of adaptive proteins in the top scoring category. The N. punctiforme genome is extraordinarily enriched in sensor histidine protein kinases (HK; 156), response regulators (RR; 103, plus 53 hybrid HK-RR proteins), and serine/threonine protein kinases (PK; 59, 12 of which are hybrid HK-PK proteins). The 306 genes putatively encoding sensory transduction proteins vastly exceed those recorded in heterotrophic bacteria. The 44 HK proteins in the proteome constituted nearly one-half (45%) of the signal transduction proteins identified. Most of the identified HKs (35) contain only prototypical kinase domains: four are hybrids with a PK domain, three hybrids have a RR receiver domain in the C terminus, and one has a RR receiver in the N terminus where it may function as a sensor. One hybrid HK-RR (NpR4769) has a pair of N-terminal RR receiver domains flanking a DNA binding domain, as well as a PAS sensing domain. One could speculate that, in this protein, the most N-terminal RR receiver functions as a sensory domain, with the phosphotransfer coming from a separate HK-P protein, thereby, in conjunction with the PAS domain, stimulating autophosphorylation in the HisK domain and intramolecular phosphotransfer via the Hpt domain to the second RR receiver domain, which then modulates DNA binding and transcriptional regulation. Biochemical assays of the purified protein could test such speculation of a single sense-response transcriptional regulatory protein. In addition to seven individual PK and four hybrid HK-PK proteins, three PK phosphatases are present. The latter proteins imply a sensitive feedback modulation of these signaling systems. The proteome contains 24 transcriptional factors, and 12 of the 20 RR proteins have DNA-binding output domains. Most of the factors are computationally identified as simply transcriptional regulatory proteins, with undefined gene targets. Thus, the soluble proteome contains about 20% of the potential transcriptional regulatory proteins putatively encoded in the Journal of Proteome Research • Vol. 5, No. 11, 2006 3101
research articles genome. Included in this group of transcriptional factors are three of the twelve group 2 alternative sigma subunits of RNA polymerase. Mutation of three alternative sigma subunits in related Anabaena sp. strain PCC 7120 did not yield definitive phenotypes.25 We conclude from these data that ammonium-grown N. punctiforme has a substantial capacity to sense and transcriptionally respond to change in the growth environment. Nevertheless, the bulk of the genome-encoded signal sensory transduction and response capacity is either present at low concentrations or requires exposure to unknown environmental conditions to trigger their expression. Essentially all heterocyst-forming cyanobacteria have the genetic information to produce cyclic substituted peptides.26 Many of these peptides are biologically active, some acting as hepatotoxins; the most common are microcystins.27,28 The products are synthesized via nonribosomal peptide synthetase and polyketide synthase proteins, involving keto- and acyltransferases, with the side chains modified by methyl-transferases and dehydrogenases. The N. punctiforme minimal proteome contains 28 proteins involved in the synthesis of cyclic peptides (Table 1). The genes encoding the detected proteins are from 7 genetic loci ranging from 16.3 to 71.9 kbp in length. These clusters represent the most distinct genetic islands in the N. punctiforme genome. The peptides produced by N. punctiforme are classified as nostopeptides and have low to no measurable toxicity.10 The specific physiological roles of these secondary metabolic products and the selective pressures on their evolution in the cyanobacteria lineage are unknown. Also present in the minimal proteome are five proteins associated with developmental events, one with akinetes and four with heterocysts (Table 1). Two of the heterocyst proteins function in signal transduction for synthesis of heterocyst wall components that occurs after the induction of differentiation: NpR1012, a HK homologue of HepK, which is involved in envelope polysaccharide synthesis;29 and NpR6193, with homology to DevH, which is annotated as a DNA binding protein, and regulates the synthesis of glycolipids.30 DevH, but not HepK, was previously shown to be constitutively expressed and enhanced following nitrogen starvation.30 The heterocystassociated proteins HetF and PatN influence both the presence and the pattern of heterocyst spacing in N. punctiforme. NpF4885 encodes HetF, which has homology to proteins with a caspase hemoglobinase fold31 and is required for HetR autoregulatory transcription; hetF mutants fail to differentiate heterocysts, and overexpression of hetF yields multiple contiguous heterocysts in the absence of ammonium.32 PatN (NpF6624) is a conserved hypothetical protein found in heterocyst-forming cyanobacteria;4 mutants differentiate multiple heterocysts singly spaced in the filaments. Both hetF32 and patN33 are constitutively transcribed at a low level in N. punctiforme. The presence of DevH, HetF, and PatN in the minimal proteome is, therefore, not unexpected. NpF5452 encodes a homologue of AvaK, a protein of unknown function that is described as specific to akinetes of Anabaena variabilis.34 Cellular localization studies imply enhanced accumulation of AvaK in akinetes, but its absence in vegetative cells.34 The presence of AvaK in the ammonium grown proteome indicates that either the localization studies were of low resolution or the accumulation profile of the AvaK homologue differs in N. punctiforme. iv. Selfish Metabolic Proteins. The 13 selfish proteins (less than 1% of the proteome) include 10 putative transposases and 3102
Journal of Proteome Research • Vol. 5, No. 11, 2006
Anderson et al.
3 sequences most highly related to phage products, including a retron-type reverse transcriptase (Table 1). The N. punctiforme genome contains over 360 active and inactive transposase genes in multiple families. The fact that 10 transposases are present in the minimal proteome implies the potential for inactivation, by a transposition event, of genes that are not under growth selection. Some cyanobacteria tend to change phenotypically during prolonged serial transfer of cultures. Nostoc species often adapt to laboratory culture by irreversible loss of the aseriate growth morphology and the differentiation of motile hormogonia,35 possibly as a result of transposition, but this has never been tested. v. Unassigned Proteins. The 608 unassigned proteins constituted the second largest category of proteins (39%) in the minimal proteome (Table 1). This value compares to the 47% open reading frames (ORFs) in the N. punctiforme genome which are classified in the unassigned category. The majority (54%) are recognized as conserved hypothetical, followed by proteins with one or more distinct domains, but unknown function (37%), and hypothetical proteins unique to N. punctiforme (10%). This fraction of unassigned proteins is greater than that recorded in well studied bacteria, such as the 14% out of the 1147 proteins detected in Escherichia coli by LC/ MS/MS.36 This difference is consistent with the multiple developmental alternatives and ecological niches of N. punctiforme compared to E. coli, and the fact that cyanobacteria, in general, lack the extended history of detailed physiological, biochemical, and genetic characterization reflective of heterotrophic bacteria. Identification of the physiological roles of the 62 expressed hypothetical proteins is of specific interest in understanding the evolution of a complex cyanobacterium. vi. Plasmid-Encoded Proteins. Plasmids appear to be a common feature of cyanobacteria,37 but their role in cyanobacterial evolution and fitness is unknown. Similar to N. punctiforme, the two other heterocyst-forming cyanobacteria whose sequenced genomes are publicly available have 4 (A. variabilis) and 5 (Anabaena PCC 7120) plasmid replicons, ranging from 5.5 to 408 kbp. The minimal proteome of N. punctiforme contains 82 plasmid encoded proteins (data not specifically summarized in tabular form), with the fewest (2) from the smallest plasmid (E; 26.14 kbp encoding 26 ORFs) and the most (36) from the largest plasmid (A; 354.56 kbp, encoding 295 ORFs). In general, based on computationally annotated ORFs, the identified proteome reflects about 12% of the coding capacity of all of the plasmids, with a range of 5% (plasmid C) to 15% (plasmid D). The most consistently represented proteins encoded by each plasmid are involved in DNA metabolism and/or chromosome partitioning. These are proteins that most likely ensure survival of the plasmid elements. One-half of the plasmid encoded proteins fall into the unassigned category and includes 11 hypothetical proteins. Although there is a diversity of plasmid encoded functional proteins present, none appear to be either not duplicated by a chromosomal gene or obviously essential for survival of the cell under the permissive ammonium-growth conditions.
Conclusions The proteome reported here is biased to proteins expressed at detectable levels, proteins susceptible to proteolysis by trypsin after denaturation, reduction and alkylation, and proteins that give informatically informative tryptic peptides of appropriate size to be sequenced by tandem mass spectrometry (ca. 5-30 residues). This work utilized a widely used
research articles
Soluble 3D LC/MS/MS Proteome
3D ion trap. With adequate care, this instrument can isolate and fragment precursor ions in the low femtomole range. The introduction of commercially available hybrid Fourier transform ion cyclotron resonance (FTICR) instruments, which detect peptides in the attomole range with increased dynamic range,38 or a highly customized FTICR instrument with zeptomole sensitivity,39 should further extend the examination of microbial (and other) proteomes. It is thus likely that the firstpass proteome defined here underestimates the number of expressed proteins, especially as membrane fractions have not been separately isolated and analyzed. However, collection of proteome-wide MS/MS spectra may in the future allow a more detailed analysis of posttranslational modifications than analyses based on precursor ion mass and chromatographic retention time. Nevertheless, the characteristics of the identified core metabolic proteins here suggests a robust identification of those proteins required by nearly all bacteria for growth and reproduction, dependent, of course, on their carbon and energy source. This first pass examination of the soluble N. punctiforme proteome has also revealed interesting information about its lifestyle. Most relevant is the presence of proteins for metabolism of reactive oxygen and photorepair of damaged DNA. By their nature, cyanobacteria produce oxygen to relatively high cellular concentrations, especially under high light intensities. It is known that cyanobacteria can encode multiple superoxide dismutases40 and other enzymes of oxidative stress, but what has not been recognized is their constitutive presence in a very permissive growth proteome, many redundant and likely at high cellular levels (Table 3). Blue light activated photorepair of DNA occurs in cyanobacteria and the process hampers selection of point mutations induced by mutagens such as UV light when mutagenized cultures are segregated in the presence of white light.41 This photorepair depends on deoxyribodipyrimidine photolyases (Phr) and not on high UV-light-induced proteins of the Uvr family. Uvr encoding genes are present in the N. punctiforme genome, and one (UvrA) was found in the proteome. Together, these observations support our suggestion that the constitutive presence of such proteins is in response to the constant exposure to high oxygen and light inherent in the cyanobacterial way of life. Although oxygenic photoautotrophy reflects the most nutritionally independent lifestyle on earth, N. punctiforme has an extraordinary genomic capacity to response to environmental signals. This response capacity would be predicted of organisms seeking a variety of carbon and energy sources, and occupying multiple habitats, but perhaps not of a photoautotroph. Approximately 30% of the potential signal transduction proteins encoded in the genome are present in the minimal proteome. Thus, N. punctiforme is poised to rapidly respond to environmental changes. The specific types of environmental changes that are sensed and the associated signal transduction pathways are largely unknown. We have suggested that the adaptive processes of multiple cellular differentiation events and symbiotic competence of N. punctiforme evolved in the cyanobacterial lineage.4 If so, homologous sequences of those regulatory proteins are absent in the genomes of other developmentally and symbiotically competent bacteria and will need to be identified by functional genomics, including proteomics and transcriptomics. The unassigned proteins identified in this proteome are obvious targets for detailed study. N. punctiforme and its relatives respond to a limitation in combined nitrogen by the differentiation of nitrogen-fixing
heterocysts. In cyanobacteria, the signal of nitrogen limitation is sensed by a Crp family transcriptional regulator, NtcA.42 We detected nearly 100 signal transduction proteins, but NtcA, which is constitutively expressed at a low level,42 was not among them, although two putative Crp proteins were present. Nevertheless, we did detect four proteins involved in regulation of patterned heterocyst differentiation and maturation. On the basis of the amounts of RNA required in Northern blots, genes encoding the unique differentiation proteins HetF32 and PatN33 appear to be constitutively expressed at a low relative level. While the transcriptional regulatory protein DevH, required for glycolipid synthesis, can be detected in protein gels,30 HepK has been considered as a late nitrogen-starvation induced protein.29 The fact that we have detected these proteins in the minimal proteome attests to the high level of resolution we obtained. We suggest it will be possible to detect, by LC/MS/ MS, modification states of some of these proteins43 and changes in both modification state and protein concentration following environmental shifts leading to the different developmental states. We are also poised to compare the N. punctiforme proteome to its transcriptome under different growth and developmental states. While mRNA microarray data are more readily obtained, extrapolation of mRNA levels to levels of expressed proteins ignores systems designed to regulate the steady-state levels of proteins, such as the ubiquitin-proteasome system of eukaryotes. Poor correlations between mRNA microarray data and proteomics examination of protein levels have been observed44-46 and may reflect significant regulatory processes that may otherwise remain undetected.
Acknowledgment. This work was supported by NSF grant MCB 0317104 to J.C.M. and at the University of Oregon by the Murdock Charitable Trust. Supporting Information Available: Supplementary Table 1 includes a list of identified Nostoc punctiforme proteins, the number of unique peptide sequences assigned to each protein, the support vector machine learning analysis-derived probability of correct sequencing for the best peptide assigned to that protein, the summed probabilities of all peptides identifying that protein, and an indicator of the number of identifying peptides that meet the Sequest filtering criteria listed in the methods section. Supplementary Table 2 lists the identified N. punctiforme proteome with annotations assigning the category of each protein and its function (if known). This material is available free of charge via the Internet at http://pubs.acs.org. References (1) Schopf, J. W.. The fossil record: tracing the roots of the cyanobacterial lineage. In The Ecology of Cyanobacteria. Their Diversity in Time and Space; Whitton, B. A., and Potts, M., Eds.; Kluwer Acad Publ.: Dordrecht, 2000; pp 13-35. (2) Des Marais, D. J. When did photosynthesis emerge on Earth? Science 2000, 1703-1705. (3) Wilmotte, A.; Herdman, M. Phylogenetic relationships among the cyanobacteria based on 16S rRNA sequences. In: Bergey’s Manual of Systematic Bacteriology, 2nd ed.; Volume One, The Archaea and the deeply branching and phototrophic bacteria. Boone, D. R., and Castenholz, R. W., Eds.; New York: Springer; 2001, pp 487-493. (4) Meeks, J.; Campbell, E.; Summers, M.; Wong, F. Cellular differentiation in the cyanobacterium Nostoc punctiforme. Arch Microbiol. 2002, 178, 395-403. (5) Fay, P. Oxygen relations of nitrogen fixation in cyanobacteria. Microbiol. Rev. 1992, 56, 340-373.
Journal of Proteome Research • Vol. 5, No. 11, 2006 3103
research articles (6) Wolk, C. P.; Ernst, A.; Elhai, J. Heterocyst metabolism and development. In The Molecular Biology of Cyanobacteria; Bryant, D. A., Ed.; Kluwer Acad. Publ.: Dordrecht, 1994; pp 769-823. (7) Meeks, J. C. Symbiotic interactions between Nostoc punctiforme, a multicellular cyanobacterium, and the hornwort Anthoceros punctatus. Symbiosis 2003, 34, 55-71. (8) Meeks, J. C. Molecular mechanisms in the nitrogen-fixing NostocBryophyte symbiosis. In Molecular Basis of Symbiosis; Overmann, J., Ed.; Springer-Verlag: Berlin, 2005; pp 165-196. (9) Meeks, J. C.; Elhai, J.; Theil, T.; Potts, M.; Larimer, F.; Lamerdin, J.; Predki, P.; Atlas, R. An overview of the genome of Nostoc punctiforme, a multicellular symbiotic cyanobacterium. Photosyn Res. 2001, 70, 85-106. (10) Hunsucker, S.; Klage, K.; Slaughter, S.; Potts, M.; Helm, R. A preliminary Investigation of the Nostoc punctiforme proteome. Biochem. Biophys. Res. Commun. 2004, 317, 1121-27. (11) Allen, M. B.; D. I. Studies on nitrogen-fixing blue-green algae I. Growth and nitrogen fixation by Anabaena cylindrica Lemm. Plant Physiol. 1995, 30, 366-372. (12) Kennedy, R.; Jorgensen, J. Preparation and evaluation of packed capillary liquid chromatography columns with inner diameters from 20 to 50 µm. Anal. Chem. 1989, 61, 1128-1135. (13) Eng, J.; McCormack, A.; Yates, J., III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989. (14) Yates, J., III; Eng, J.; McCormack, A. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal. Chem. 1995, 67, 3202-3210. (15) Olsen, J.; Ong, S.; Mann, M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell Proteomics 2004, 3, 608. (16) Anderson, D. C.; Li, W.; Payan, D. G.; Noble, W. S. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: Support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res. 2003, 2, 137-146. (17) Washburn, M.; Wolters, D.; Yates, J., III. Large scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 2001, 19, 242-247. (18) Platt, J. C. Probabilistic outputs for support vector machines and comparisons to regularized likelihood methods. In Advances in Large Margin Classifiers; Smola, A., Bartlett, P., Scholkopf, B., Schuurmans, D., Eds.; MIT Press: Cambridge, MA, 1999; pp 6174. (19) Schaecher, M.; Ingraham, J. L.; Neidhardt, F. C. Microbe; American Society of Microbiology: Washington, D. C., 2005; pp 1-530. (20) Meeks, J. et al. Manuscript in preparation. (21) Summers, M. L.; Wallis, J. G.; Campbell, E. L.; Meeks, J. C. Genetic evidence of a major role for glucose-6-phosphate dehydrogenase in nitrogen fixation and dark growth of the cyanobacterium Nostoc sp. strain ATCC 29133. J. Bacteriol. 1995, 177, 6184-6194. (22) Cohen-Bazire, G.; Bryant, D. A. Phycobilisomes: composition and structure. In The Biology of Cyanobacteria; Carr, N. G., Whitton, B. A., Eds.; Blackwell: Oxford, 1982; pp 143-190. (23) Hayes J.; Flanagan J.; Jowsey I. Glutathione transferases. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 51-88. (24) McCord J.; Fridovich, I. The biology and pathology of oxygen radicals. Ann. Intern. Med. 1978, 89, 122-127. (25) Khudyakov, I. Y.; Golden, J. W. 2001. Identification and inactivation of three group 2 sigma factor genes in Anabaena sp. strain PCC 7120. J. Bacteriol. 2001, 183, 6667-6675. (26) Christian, G.; Dittmen, E.; Ordorika, L. V.; Rippka, R.; Herdman, M.; Borner, T. Nonribosomal peptide synthetase genes occur in most cyanobacteria genera as evidenced by their distribution in axenic strains of the PCC. Arch. Microbiol. 2001, 176, 452-458. (27) Babica, P.; Blaha, L.; Marsalek, B. Exploring the natural role of microcystins - a review of effects on photoautotrophic organisms. J. Phycol. 2006, 42, 9-20. (28) Oksanen, I.; Jokela, J.; Fewer, D.; Wahlsten, M.; Rikkinen, J.; Sivonen, K. Discovery of Rare and Highly Toxic Microcystins from Lichen-Associated cyanobacterium Nostoc sp. Strain IO-102-I. Appl. Env. Microbiol. 2004, 70, 5756-5763.
3104
Journal of Proteome Research • Vol. 5, No. 11, 2006
Anderson et al. (29) Zhou, R.; Wolk, C. P. A two-component system mediates developmentally regulated biosynthesis of a heterocyst polysaccharide. J. Biol. Chem. 2003, 278, 19939-19946. (30) Ramirez, M. E.; Hebbar, P. B.; Zhou, R.; Wolk, C. P.; Curtis, S. E. Anabaena sp. strain PCC 7129 gene devH is required for synthesis of the heterocyst glycolipid layer. J. Bacteriol. 2005, 187, 23262331. (31) Aravid, l.; Koonin, E. V. Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of eukaryotic separins. Proteins 2002, 46, 355-367. (32) Wong, F.; Meeks, J. C. ThehetF gene product is essential to heterocyst differentiation and affects HetR function in the cyanobacterium Nostoc punctiforme. J. Bacteriol. 2001, 183, 26542661. (33) Wong, F.; Meeks, J. C., unpublished observations. (34) Zhou, R.; Wolk, C. P. Identification of an akinete marker gene in Anabaena variabilis. J. Bacteriol. 2002, 184, 2529-2532. (35) Rippka, R.; Castenholz, R. W.; Herdman, M. Subsection IV. In Bergey’s Manual of Systematic Bacteriology, 2nd ed.; Volume One, The Archaea and the deeply branching and phototrophic bacteria; Boone, D. R., Castenholz, R. W., Eds.; Springer, New York, 2001; pp 562-589. (36) Corbin, R. W.; Paily, O.; Yang, F.; Shabanowitz, J.; Platt, M.; Lyons, C. E., Jr.; Root, K.; McAuliffe, J.; Jordan, M. I.; Kustu, S.; Soupene, E.; Hunt, D. F. 2003. Toward a protein profile of Escherichia coli: comparison to its transcripton profile. Proc. Natl. Acad. Sci. U.S.A. 100, 9232-9237. (37) Houmard, J.; Tandeau de Marsac, N. Cyanobacterial genetic tools: current status. Methods Enzymol. 1988, 167, 808-847. (38) Syka, J.; Marto, J.; Bai, D.; Horning, S.; Senko, M.; Schwartz, J.; Ueberheide, B.; Garcia, B.; Busby, S.; Muratore, T.; Shabanowitz, J.; Hunt, D. F. Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 2004, 3, 621-626. (39) Shen, Y.; Tolic, N.; Masselon, C.; Pasa-Tolic, L.; Camp, D.; Hixson, K.; Zhao, R.; Anderson, G.; Smith, R. D. Ultrasensitive proteomics using high- efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal. Chem. 2004, 76, 144-154. (40) Regelsberger, G.; Atzenhofer, W.; Ruker, F.; Peschek, G. A.; Jakopitsch, C.; Paumann, M.; Furtmuller, P. G.; Obinger, C. Biochemical characterization of a membrane bound manganesecontaining superoxide dismutase from the cyanobacterium Anabaena PCC 7120. J. Biol. Chem. 2002, 277, 43615-43622. (41) Golden, S. S. Mutagenesis of cyanobacteria by classical and genetransfer based methods. Method Enzymol. 1988, 167, 714-727. (42) Herrero, A.; Muro-Pastor, A. M.; Flores, E. Nitrogen control in cyanobacteria. J. Bacteriol. 2001, 183, 411-425. (43) Rhee S.; Yang K.; Kang S.; Woo H.; Chang T. Controlled elimination of intracellular H(2)O(2): regulation of peroxiredoxin, catalase, and glutathione peroxidase via post-translational modification. Antioxid. Redox Signal. 2005, 7, 619-626. (44) Griffin, T.; Gygi, S.; Ideker, T.; Rist, B.; Eng, J.; Hood, L.; Aebersold, R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics 2002, 1, 323-333. (45) Conrads, K.; Yi, M.; Simpson, K.; Lucas, D.; Camalier, C.; Yu, L.; Veenstra, T.; Stephens, R.; Conrads, T.; Beck, G. A Combined Proteome and Microarray Investigation of Inorganic Phosphateinduced Pre-osteoblast Cells. Mol. Cell Proteomics 2005, 4, 12841296. (46) Kuo, C.; Kuo, C.; Liang, C.; Liang, S. A transcriptomic and proteomic analysis of the effect of CpG-ODN on human THP-1 monocytic leukemia cells. Proteomics 2005, 5, 894-906.
PR060272M
