Functional Diversity Of Proteins Research Articles

Functions of intrinsic disorder in proteins involved in DNA demethylation during pre-implantation embryonic development

DNA demethylation is involved in many biological processes during pre-implantation embryonic development in mammals. To date, the complicated mechanism of DNA demethylation is still not fully understood. Ten-eleven translocation family (TET3, TET1 and TET2), thymine DNA glycosylase (TDG) and DNA methyltransferase 1 (DNMT1) are considered the major protein enzymes of DNA demethylation in pre-implantation embryos. TET3, TET1, TET2, TDG, and DNMT1 contain abundant levels of intrinsically disordered protein regions (IDPRs), which contribute to increasing the functional diversity of proteins. Thus we tried to explore the complicated DNA demethylation in pre-implantation embryos from the intrinsic disorder perspective. These five biological macromolecules all have DNA demethylation-related functional domains. They can work together to fulfill DNA demethylation in pre-implantation embryos through complex protein–protein interaction networks. Intrinsic disorder analysis results showed these proteins were partial intrinsically disordered proteins. Many identifiable disorder-based DNA-binding sites, protein-binding sites and post-translational modification sites located in the intrinsically disordered regions, and DNA demethylation deficiency point mutations in the IDPRs could significantly change the local disorder propensity of these proteins. To the best of our knowledge, this work provides a new viewpoint for studying the mechanism of DNA methylation reprogramming during mammalian pre-implantation embryonic development.

Virus-Inspired Function in Engineered Protein Cages.

The structural and functional diversity of proteins combined with their genetic programmability has made them indispensable modern materials. Well-defined, hollow protein capsules have proven to be particularly useful due to their ability to compartmentalize macromolecules and chemical processes. To this end, viral capsids are common scaffolds and have been successfully repurposed to produce a suite of practical protein-based nanotechnologies. Recently, the recapitulation of viromimetic function in protein cages of nonviral origin has emerged as a strategy to both complement physical studies of natural viruses and produce useful scaffolds for diverse applications. In this perspective, we review recent progress toward generation of virus-like behavior in nonviral protein cages through rational engineering and directed evolution. These artificial systems can aid our understanding of the emergence of viruses from existing cellular components, as well as provide alternative approaches to tackle current problems, and open up new opportunities, in medicine and biotechnology.

The seven transmembrane domain protein MoRgs7 functions in surface perception and undergoes coronin MoCrn1-dependent endocytosis in complex with Gα subunit MoMagA to promote cAMP signaling and appressorium formation in Magnaporthe oryzae.

Regulator of G-protein signaling (RGS) proteins primarily function as GTPase-accelerating proteins (GAPs) to promote GTP hydrolysis of Gα subunits, thereby regulating G-protein mediated signal transduction. RGS proteins could also contain additional domains such as GoLoco to inhibit GDP dissociation. The rice blast fungus Magnaporthe oryzae encodes eight RGS and RGS-like proteins (MoRgs1 to MoRgs8) that have shared and distinct functions in growth, appressorium formation and pathogenicity. Interestingly, MoRgs7 and MoRgs8 contain a C-terminal seven-transmembrane domain (7-TM) motif typical of G-protein coupled receptor (GPCR) proteins, in addition to the conserved RGS domain. We found that MoRgs7, but not MoRgs8, couples with Gα MoMagA to undergo endocytic transport from the plasma membrane to the endosome upon sensing of surface hydrophobicity. We also found that MoRgs7 can interact with hydrophobic surfaces via a hydrophobic interaction, leading to the perception of environmental hydrophobiccues. Moreover, we found that MoRgs7-MoMagA endocytosis is regulated by actin patch-associated protein MoCrn1, linking it to cAMP signaling. Our studies provided evidence suggesting that MoRgs7 could also function in a GPCR-like manner to sense environmental signals and it, together with additional proteins of diverse functions, promotes cAMP signaling required for developmental processes underlying appressorium function and pathogenicity.

Antidepressants are modifiers of lipid bilayer properties.

The two major classes of antidepressants, tricyclic antidepressants (TCAs) and selective serotonin reuptake inhibitors (SSRIs), inhibit neurotransmitter reuptake at synapses. They also have off-target effects on proteins other than neurotransmitter transporters, which may contribute to both desired changes in brain function and the development of side effects. Many proteins modulated by antidepressants are bilayer spanning and coupled to the bilayer through hydrophobic interactions such that the conformational changes underlying their function will perturb the surrounding lipid bilayer, with an energetic cost (ΔG def) that varies with changes in bilayer properties. Here, we test whether changes in ΔG def caused by amphiphilic antidepressants partitioning into the bilayer are sufficient to alter membrane protein function. Using gramicidin A (gA) channels to probe whether TCAs and SSRIs alter the bilayer contribution to the free energy difference for the gramicidin monomer⇔dimer equilibrium (representing a well-defined conformational transition), we find that antidepressants alter gA channel activity with varying potency and no stereospecificity but with different effects on bilayer elasticity and intrinsic curvature. Measuring the antidepressant partition coefficients using isothermal titration calorimetry (ITC) or cLogP shows that the bilayer-modifying potency is predicted quite well by the ITC-determined partition coefficients, and channel activity is doubled at an antidepressant/lipid mole ratio of 0.02-0.07. These results suggest a mechanism by which antidepressants could alter the function of diverse membrane proteins by partitioning into cell membranes and thereby altering the bilayer contribution to the energetics of membrane protein conformational changes.

α2-HS Glycoprotein in Plasma Extracellular Vesicles Inhibits the Osteogenic Differentiation of Human Mesenchymal Stromal Cells In Vitro.

Extracellular vesicles (Evs) contain diverse functional proteins, mRNAs, miRNAs, and DNA fragments, are secreted by various types of cells, and play important roles in cellular communication. Here, we show for the first time that plasma Evs inhibited the osteogenic differentiation of mesenchymal stromal cells (MSCs) in vitro and the level of inhibition was positively correlated with the plasma Evs concentration. Plasma Evs downregulated the expression of markers such as osteocalcin (OCN), Runt-related transcription factor 2 (Runx2), and Osterix at mRNA levels required for osteogenic differentiation and reduced pSmad1/5/8 levels in MSCs. Furthermore, pSmad1/5/8 levels increased and MSCs underwent normal osteogenic differentiation after Evs-derived α2-HS glycoprotein (AHSG) function was inhibited with an anti-AHSG neutralizing antibody. However, the levels of pERK1/2, active β-catenin, and HES1 were not significantly altered. Therefore, we propose that as essential components of the extracellular microenvironment of MSCs, plasma Evs are taken up by MSCs and subsequently repress osteogenic differentiation through an AHSG-mediated decrease in pSmad1/5/8 levels. Our work identifies plasma Evs as novel regulators of MSC osteogenic differentiation.

Distinct mechanisms of substrate selectivity in the DRE-TIM metallolyase superfamily: A role for the LeuA dimer regulatory domain

The use of modular domains in proteins affords nature a simple route to the diversification of protein function, but co-evolution between domains can complicate large-scale functional annotation. The LeuA dimer regulatory domain is primarily responsible for allosteric feedback inhibition of the enzymes isopropylmalate synthase (IPMS) and citramalate synthase (CMS). In addition to this regulatory role, presence of the domain may also affect substrate selectivity in certain members of the enzyme family. To assess the role of the LeuA dimer regulatory domain in substrate selectivity, truncated versions of IPMS and CMS from Methanococcus jannaschii (MjIPMS and MjCMS, respectively) have been created that lack the LeuA dimer regulatory domain. In the case of MjIPMS, loss of the regulatory domain does not affect substrate selectivity, consistent with previous reports identifying conserved active site residues that play this role. Loss of the regulatory domain in MjCMS, however, results in increased functional promiscuity. Both truncated enzymes exhibit a shift in quaternary structure from tetrameric to monomeric forms as judged by size-exclusion chromatography. Kinetic isotope effects reveal that loss of the regulatory domain results in unique effects on catalysis with chemistry becoming more rate-determining in MjIPMS and less rate-determining in MjCMS. Finally, substitution of conserved active site residues in the promiscuous truncated MjCMS affect substrate selectivity while identical substitutions cause no changes in the wild-type enzyme. Overall, the data predicts a more complex role for the LeuA dimer regulatory domain in substrate selectivity through catalytic modulations rather than selectivity through differential binding as a result of extensive co-evolution between the catalytic and regulatory domains.

Micronemal protein 13 contributes to the optimal growth of Toxoplasma gondii under stress conditions.

Toxoplasma gondii is a ubiquitous parasitic protozoan infecting humans and a wide variety of animals. Fast-replicating tachyzoites during acute infection and slowly growing bradyzoites during chronic infection are the two basic forms of T. gondii in intermediate hosts. Interconversion between the two contributes to the transmission and pathogenesis of this parasite. Secretory micronemal proteins are thought to mediate interactions with host cells and facilitate parasite invasion, therefore the majority of them are highly expressed in tachyzoites. Micronemal protein 13 (MIC13) is unique in that its expression is low in tachyzoites and is upregulated under bradyzoite-inducing conditions. Previous attempts to disrupt this gene were not successful, implying that it may play critical roles during parasite growth. However, in this study, MIC13 was successfully disrupted in type 1 strain RH and type 2 strain ME49 using CRISPR/Cas9-mediated gene disruption techniques. Consistent with its low expression in tachyzoites and increased expression under stress or bradyzoite-inducing conditions, MIC13-inactivated mutants displayed normal growth, host cell invasion, intracellular replication, and egress, as well as acute virulence at the tachyzoite stage. However, under stress conditions, such as high pH or oxygen limitation, MIC13-disrupted parasites showed significantly slower growth rates compared to the parental strains, suggesting that it is required for optimal parasite growth under bradyzoite-inducing or stress conditions. This is the first micronemal protein reported to have such expression pattern and function modes, which expands our understanding of the diverse functions of micronemal proteins.

BMP6 increases TGF-β1 production by up-regulating furin expression in human granulosa-lutein cells

Bone morphogenetic protein 6 (BMP6) and transforming growth factor-β1 (TGF-β1) are key intraovarian regulators that play essential roles in regulating mammalian follicular function and promoting oocyte maturation. Furin, a member of the subtilisin-like proprotein convertase family, promotes the activation of diverse functional proteins by cleaving protein precursors in the secretory pathway. The aim of this study was to investigate the effect and underlying molecular mechanisms by which BMP6 regulates the expression of furin to increase TGF-β1 production. Primary and immortalized (SVOG) human granulosa-lutein (hGL) cells were used as study models. Our results show that BMP6 significantly up-regulated the expression of furin and increased the production of TGF-β1 in hGL cells. Using dual inhibition approaches (kinase receptor inhibitors and small interfering RNA-targeted knockdown), we demonstrate that both activin receptor-like (ALK)2 and ALK3 are involved in the BMP6-induced up-regulation of furin. Additionally, knockdown of furin abolished BMP6-induced increases in TGF-β1 production. Moreover, knockdown of endogenous SMAD4 reversed the BMP6-induced increase in furin expression. These results indicate that the ALK2/3-mediated canonical SMAD signaling pathway is required for the stimulatory effect of BMP6 on furin expression, which in turn increases the production of TGF-β1 in hGL cells. Our findings provide insights into the molecular interactions and mechanisms of two intrafollicular growth factors in hGL cells.

Transient Expression of ESCRT Components in Arabidopsis Root Cell Suspension Culture-Derived Protoplasts.

Localization studies are important to understand the function of diverse proteins. The endosomal trafficking pathway is very complex, and a lot of proteins function in this pathway, primarily the endosomal sorting complexes required for transport (ESCRTs). Some of the ESCRT-related proteins or mutant variants cannot be stably expressed in planta due to the toxicity of their expression. Therefore, a transient expression system is necessary to study their function. Transient expression in protoplasts from Arabidopsis root cell-derived culture serves as a fast and reliable method for the expression and cell biological and biochemical analyses of otherwise toxic constructs.

Data-Independent Acquisition for Yeast Glycoproteomics.

Glycosylation is a complex posttranslational modification that is critical for regulating the functions of diverse proteins. Analysis of protein glycosylation is made challenging by the high degree of heterogeneity in both glycan occupancy and structure. Here, we describe methods for data-independent acquisition (SWATH) mass spectrometry analysis of structure and occupancy of N-glycans from yeast cell wall glycoproteins.

Superoxide dismutase transcellular shuttle constructed from dendritic MOF and charge reversible protein derivatives.

The development of molecular biology has led to the identification of protein-based therapeutics as an intriguing approach for the treatment of a wide range of diseases. To manufacture transcellular protein delivery shuttles, we attempted charge reversal chemistry on native proteins [e.g., superoxide dismutase (SOD): an enzyme capable of scavenging detrimental reactive oxygen species] by the selective conversion of the positively charged amino residues of native SOD to conjugated negatively charged citraconic moieties, eliciting overall negatively charged polyelectrolytes for the subsequent electrostatic self-assembly with cationic metal-organic framework (MOF) derivatives into protein delivery systems. Please note that the charge conversion was reversible, restoring the original amino groups in intracellular acidic endosome compartments (pH 5), which afforded facile charge reversible functions to reclaim the active SOD in the cell interior. In particular, the strategic manufacture of dendritic MOF supramolecular architectures as transcellular shuttles for the aforementioned charge-reversible SOD derivatives is noteworthy. The MOF was surface-functionalized with several polycationic segments, thus contributing to the hyper-charged architecture for the easy accommodation of the negatively charged SOD derivatives. Consequently, the SOD derivatives managed to internalize into cells by hitchhiking via endocytosis of the positively charged MOF. Once they resided in the acidic endosomes, the charge reversal of the SOD derivatives could occur smoothly and result in reduced interactions between the charged-reversed SOD and MOF, leading to the release of active SOD. Simultaneously, the dendritic MOF due to protein release presented a highly positive-charged architecture to provoke endosome membrane disruption, consequently spurring the translocation of SOD to the cytosol for the execution of its enzymatic activities. Herein, the intracellular ROS level of the activated macrophages was validated to be markedly suppressed by our proposed transcellular SOD shuttles, thereby indicating their wide availability to diverse functional proteins for biomedical applications.

Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides

We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.

Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope.

The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life - Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.

Programmable and printable Bacillus subtilis biofilms as engineered living materials.

Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.

A Membraneless Organelle Associated with the Endoplasmic Reticulum Enables 3′UTR-Mediated Protein-Protein Interactions

Approximately half of human genes generate mRNAs with alternative 3' untranslated regions (3'UTRs). Through 3'UTR-mediated protein-protein interactions, alternative 3'UTRs enable multi-functionality of proteins with identical amino acid sequence. While studying how information on protein features is transferred from 3'UTRs to proteins, we discovered that the broadly expressed RNA-binding protein TIS11B forms a membraneless organelle, called TIS granule, that enriches membrane protein-encoding mRNAs with multiple AU-rich elements. TIS granules form a reticular meshwork intertwined with the endoplasmic reticulum (ER). The association between TIS granules and the ER creates a subcellular compartment-the TIGER domain-with a biophysically and biochemically distinct environment from the cytoplasm. This compartment promotes 3'UTR-mediated interaction of SET with membrane proteins, thus allowing increased surface expression and functional diversity of proteins, including CD47 and PD-L1. The TIGER domain is a subcellular compartment that enables formation of specific and functionally relevant protein-protein interactions that cannot be established outside.

Promotion of Myoblast Differentiation by Fkbp5 via Cdk4 Isomerization

SUMMARYFkbp5 is a widely expressed peptidyl prolyl isomerase that serves as a molecular chaperone through conformational changes of binding partners. Although it regulates diverse protein functions, little is known about its roles in myogenesis. We found here that Fkbp5 plays critical roles in myoblast differentiation through two mechanisms. First, it sequesters Cdk4 within the Hsp90 storage complex and prevents the formation of the cyclin D1-Cdk4 complex, which is a major inhibitor of differentiation. Second, Fkbp5 promotes cis-trans isomerization of the Thr172-Pro173 peptide bond in Cdk4 and inhibits phosphorylation of Thr172, an essential step for Cdk4 activation. Consistent with these in vitro findings, muscle regeneration is delayed in Fkbp5−/− mice. The related protein Fkbp4 also sequesters Cdk4 within the Hsp90 complex but does not isomerize Cdk4 or induce Thr173 phosphorylation despite its highly similar sequence. This study demonstrates protein isomerization as a critical regulatory mechanism of myogenesis by targeting Cdk4.

BMP6 Increases TGF-Beta1 Production by Up-Regulating Furin Expression in Human Granulosa-Lutein Cells

Background: Bone morphogenetic protein 6 (BMP6) and transforming growth factor--β1 (TGF--β1) are key intraovarian regulators that play essential roles in regulating mammalian follicular function and promoting oocyte maturation. Dysregulated BMP6 or TGF-β1 signaling is associated with polycystic ovary syndrome. Furin is a proprotein convertase that promotes the activation of diverse functional proteins by cleaving protein precursors. Methods: Primary and immortalized (SVOG) human granulosa-lutein (hGL) cells were used as study models. RT-qPCR, western blot analyses, and enzyme immunoassay were used to examine the effects of recombinant human BMP6 on the expression of furin and production of TGF-β1. Dual inhibition approaches (kinase receptor inhibitors and small interfering RNAs targeted knockdown) were used to investigate the underlying molecular mechanisms by which BMP6 regulated the expression of furin. Findings: BMP6 significantly up-regulated the expression of furin and increased the production of TGF-β1. Additionally, both activin receptor-like (ALK)2 and ALK3 were involved in BMP6-induced up-regulation of furin. Furthermore, knockdown of furin abolished BMP6-induced increases in TGF--β1 production, and knockdown of endogenous SMAD4 reversed the increase in furin expression induced by BMP6. Interpretation: The ALK2/3-mediated canonical SMAD signaling pathway is required for the stimulatory effect of BMP6 on furin expression, which in turn increases the production of TGF-β1 in hGL cells. Our findings shed insights into the molecular interactions and mechanisms of two intrafollicular growth factors in hGL cells, which could be potentially applied as therapeutic targets for patients with polycystic ovary syndrome. Funding Statement: Canadian Institutes of Health Research Foundation Scheme Grant #143317. Declaration of Interests: The authors have no conflict of interests to declare. Ethics Approval Statement: All participants signed a written informed consent. The study was approved by Research Ethics Board from the University of British Columbia.

Microorganismos del corredor marino Isla del Coco-Galápagos: diversidad funcional y de especies

El corredor marino Isla del Coco-Galápagos, en su conjunto, constituye un santuario para la protección de especies marinas en la región oriental del Pacífico Tropical. La alta biodiversidad de macroorganismos ha sido estudiada por décadas, sin embargo, la diversidad de microorganismos del fitoplancton, que constituyen el sustento de la vida en este ecosistema, no se conoce al mismo nivel de detalle. En este trabajo utilizamos datos metagenómicos de libre acceso para examinar la diversidad funcional de proteínas y de especies microbianas presentes en seis puntos de este corredor marino. Se identificó una altísima diversidad de microorganismos que comprende 2132 géneros distribuidos en 68 filos taxonómicos (6 Archaea, 33 Eukaryota, 38 Bacteria y 1 Virus). En particular, los taxones más abundantes fueron Candidatus Pelagibacter, Prochlorococcus, Synechococcus, el Fago T4 y Pseudomonas, los cuales coexisten con una gran cantidad de organismos poco representados. Por similitud en su composición, las comunidades pelágicas y litorales pudieron agruparse, sin embargo, estadísticamente no hubo diferencias significativas entre todas las comunidades del corredor. Este trabajo resalta la importancia ecológica del fitoplancton para el ecosistema y representa una justificación adicional protección del corredor en su conjunto.

989P - Identification research and application for protein phosphorylation modification sites in human ovarian carcinoma

Background: Phosphorylation modification, as one kind of protein post-translational modification (PTM), increases the diverse protein functions, such as cell signaling, protein folding, enzymatic activity, protein degradation, and their subcellular location. However, the subcellular phophoproteomic of ovarian carcinoma mitochondrial proteins has not been elucidated. Methods: Here, an 8-plex isobaric tag for relative and absolute quantification (iTRAQ) proteomics was used to identify mitochondrial expressed proteins (mtEPs) and phosphorylation modification sites of ovarian carcinomas relative to controls, followed by bioinformatics analysis. Results: The iTRAQ-based proteomics identified 5115 proteins and 99 phosphorylated proteins with quantitative information from purified mitochondrial samples, and 262 proteins were significantly related to overall survival in ovarian cancer patients. Interestingly, the results demonstrated that cancer cells exhibit an increased dependence on lipid metabolism, such as biosynthesis of unsaturated fatty acids, butanoate metabolism, fatty acid degradation, fatty acid metabolism, which might play an important role in ovarian carcinoma invasion and metastasis. Moreover 33 proteins related to lipid metabolism as potential markers for the development of ovarian carcinoma were identified.Additionally, 3 drug-associated phosphorylation proteins and 3 phosphorylation proteins as tumor markers in the plasma were obtained. The 99 phosphorylated proteins and TCGA data were integarated, thus obtained 9 important proteins. Among those, HSP60 were highly related with lipid metabolism. In cells with increased Hsp60 levels both the amounts of total mitochondrial short-chain acyl-CoA dehydrogenase (ACADS) proteins and folded ACADS were increased, which may influence mitochondrial protein folding and lipid metabolism. Conclusions: The current study provides a large-scale mitochondrial proteomic profiling and mitochondrion phosphoproteome with quantitative information, a certain number of proteins with the potential biomarkers, drug targets and a novel vision in the lipid metabolism bio-mechanism of human ovarian carcinoma. Legal entity responsible for the study: Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University. Funding: Xiangya Hospital Funds for Talent Introduction (to XZ), the grants from China “863” Plan Project (Grant No. 2014AA020610-1 to XZ), the National Natural Science Foundation of China (Grant No. 81272798 and 81572278 to XZ), and the Hunan Provincial Natural Science Foundation of China (Grant No. 14JJ7008 to XZ). Disclosure: All authors have declared no conflicts of interest.

Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms

Cell disruption and protein solubilization protocols for the relative quantification of individual subunits in photosystems were developed for photosynthetic organisms including cyanobacterium Synechocystis sp. PCC 6803, green-algae Chlamydomonas reinhardtii, and seed plant Arabidopsis thaliana. The optimal methods for the disruption of Chlamydomonas, Synechocystis, and Arabidopsis cells were sonication, microbeads (Φ approximately 0.1mm), and large beads (Φ=5.0mm), respectively. Extraction of the total proteins exceeded 90% using each optimal cell disruption method. Solubilization efficiency of membrane proteins was improved by the phase transfer surfactant (PTS) method. Ninety seven and 114 proteins from Chlamydomonas and Synechocystis, respectively, including membrane proteins such as photosystem proteins, ATP synthase, and NADH dehydrogenase, were successfully analyzed by nano-liquid chromatography tandem mass spectrometry. These results also indicated the improved efficiency of solubilization and trypsin digestion using PTS buffer. The results of the relative quantitative evaluation of photosystem subunits in Chlamydomonas and Synechocystis grown under high-light conditions were consistent with those of previous studies. Thus, the optimal cell disruption and PTS methods allow for comprehensive relative quantitative proteome analysis of photosynthetic organisms. Additionally, NdhD1 and NdhF1, which are NDH-1 subunit homologs, were increased under high-light conditions, suggesting that the NDH-1L complex, including NdhD1 and NdhF1, is increased under high-light conditions. The relative quantitative proteome analysis of individual subunits indicates the diverse functions of NDH-1 protein.