Abstract
The present chapter summarizes the current status of proteome research on barley. The importance of barley as a model for cereals and as a major crop is reflected by a large number of publications using proteomics as an approach to address fundamental or applied research questions. Progress through technological developments in mass spectrometry, the central analytical technique in proteomics, forms the background methodology applied for protein or peptide separation and protein identification as outlined in the first section. The grain is of central relevance for the use of barley as a crop and seed biology is a central topic in plant science. Hence, a large number of studies focus on the grain proteome as well as the changes in proteome composition during grain maturation and germination. Separate sections cover research on abiotic and biotic stress defence responses. The next section is dedicated to subcellular proteomics, isolation of organelles or subcellular fractions being a powerful strategy to cope with the complexity of the plant proteome. Typical current analytical tools can cover only a small fraction of the complete proteome. With regard to the number of genes, any proteome is increased in complexity by a high number of post-translational modifications and many potential splicing variants. In addition, the dynamic range of the individual protein abundance covers many orders of magnitude exceeding the limits of current detection methods. Although this complexity of the proteome is demanding for in-depth protein analysis, information on, e.g. post-translational modifications cannot be derived from other approaches such as transcriptomics. These aspects and potential developments are addressed in the final section of our contribution.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Al-Daoude A, Arabi MIE, Shoaib A, Jawhar M (2015) Protein variation identified in resistant and susceptible barley genotypes infected with Cochliobolus sativus. Phyton-Annales Rei Botan 55:149–158
Alexander RD, Morris PC (2006) A proteomic analysis of 14-3-3 binding proteins from developing barley grains. Proteomics 6:1886–1896
Alikhani M, Khatabi B, Sepehri M, Nekouei MK, Mardi M, Salekdeh GH (2013) A proteomics approach to study the molecular basis of enhanced salt tolerance in barley (Hordeum vulgare L.) conferred by the root mutualistic fungus Piriformospora indica. Mol BioSyst 9:1498–1510
Ashoub A, Beckhaus T, Berberich T, Karas M, Bruggemann W (2013) Comparative analysis of barley leaf proteome as affected by drought stress. Planta 237:771–781
Ashoub A, Baeumlisberger M, Neupaertl M, Karas M, Bruggemann W (2015) Characterization of common and distinctive adjustments of wild barley leaf proteome under drought acclimation, heat stress and their combination. Plant Mol Biol 87:459–471
Baginsky S (2016) Protein phosphorylation in chloroplasts—a survey of phosphorylation targets. J Exp Bot 67:3873–3882
Bak-Jensen KS, Laugesen S, Roepstorff P, Svensson B (2004) Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry. Proteomics 4:728–742
Barba-Espin G, Dedvisitsakul P, Hagglund P, Svensson B, Finnie C (2014) Gibberellic acid-induced aleurone layers responding to heat shock or tunicamycin provide insight into the N-glycoproteome, protein secretion, and endoplasmic reticulum stress. Plant Physiol 164:951–965
Bindschedler LV, Burgis TA, Mills DJS, Ho JTC, Cramer R, Spanu PD (2009) In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. hordei. Mol Cell Proteomics 8:2368–2381
Bonsager BC, Finnie C, Roepstorff P, Svensson B (2007) Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues. Proteomics 7:4528–4540
Borén M, Larsson H, Falk A, Jansson C (2004) The barley starch granule proteome—internalized granule polypeptides of the mature endosperm. Plant Sci 166:617–626
Chmielewska K, Rodziewicz P, Swarcewicz B, Sawikowska A, Krajewski P, Marczak L, Ciesiolka D, Kuczynska A, Mikolajczak K, Ogrodowicz P, Krystkowiak K, Surma M, Adamski T, Bednarek P, Stobiecki M (2016) Analysis of drought-induced proteomic and metabolomic changes in barley (Hordeum vulgare L.) leaves and roots unravels some aspects of biochemical mechanisms involved in drought tolerance. Front Plant Sci. https://doi.org/10.3389/fpls.2016.01108
Chmielowska-Bak J, Gzyl J, Rucinska-Sobkowiak R, Arasimowicz-Jelonek M, Deckert J (2014) The new insights into cadmium sensing. Front Plant Sci. https://doi.org/10.3389/fpls.2014.00245
Daneri-Castro SN, Svensson B, Roberts TH (2016) Barley germination: Spatio-temporal considerations for designing and interpreting ‘omics’ experiments. J Cereal Sci 70:29–37
Eggert K, Pawelzik E (2011) Proteome analysis of Fusarium head blight in grains of naked barley (Hordeum vulgare subsp. nudum). Proteomics 11:972–985
Endler A, Meyer S, Schelbert S, Schneider T, Weschke W, Peters SW, Keller F, Baginsky S, Martinoia E, Schmidt UG (2006) Identification of a vacuolar sucrose transporter in barley and arabidopsis mesophyll cells by a tonoplast proteomic approach. Plant Physiol 141:196–207
Endler A, Reiland S, Gerrits B, Schmidt UG, Baginsky S, Martinoia E (2009) In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach. Proteomics 9:310–321
Eubel H, Jansch L, Braun HP (2003) New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II. Plant Physiol 133:274–286
Fatehi F, Hosseinzadeh A, Alizadeh H, Brimavandi T, Struik PC (2012) The proteome response of salt-resistant and salt-sensitive barley genotypes to long-term salinity stress. Mol Biol Rep 39:6387–6397
Fatehi F, Hosseinzadeh A, Alizadeh H, Brimavandi T (2013) The proteome response of Hordeum spontaneum to salinity stress. Cereal Res Commun 41:78–87
Fenn JB (2003) Electrospray wings for molecular elephants (Nobel lecture). Angew Chem (International Edition) 42:3871–3894
Finnie C, Steenholdt T, Noguera OR, Knudsen S, Larsen J, Brinch-Pedersen H, Holm PB, Olsen O, Svensson B (2004) Environmental and transgene expression effects on the barley seed proteome. Phytochemistry 65:1619–1627
Finnie C, Bagge M, Steenholdt T, Ostergaard O, Bak-Jensen K, Backes G, Jensen A, Giese H, Larsen J, Roepstorff P, Svensson B (2009) Integration of the barley genetic and seed proteome maps for chromosome 1H, 2H, 3H, 5H and 7H. Funct Integr Genomics 9:135–143
Finnie C, Sultan A, Grasser KD (2011) From protein catalogues towards targeted proteomics approaches in cereal grains. Phytochemistry 72:1145–1153
Flodrová D, Salplachta J, Benkovska D, Bobalova J (2012) Application of proteomics to hordein screening in the malting process. Eur J Mass Spectrom 18:323–332
Focke M, Gieringer E, Schwan S, Jansch L, Binder S, Braun HP (2003) Fatty acid biosynthesis in mitochondria of grasses: malonyl-coenzyme A is generated by a mitochondrial-localized acetyl-coenzyme A carboxylase. Plant Physiol 133:875–884
Frigerio S, Campoli C, Zorzan S, Fantoni LI, Crosatti C, Drepper F, Haehnel W, Cattivelli L, Morosinotto T, Bassi R (2007) Photosynthetic antenna size in higher plants is controlled by the plastoquinone redox state at the post-transcriptional rather than transcriptional level. J Biol Chem 282:29457–29469
Görg A, Postel W, Domscheit A, Gunther S (1988) Two-dimensional electrophoresis with immobilized pH gradients of leaf proteins from barley (Hordeum vulgare)—method, reproducibility and genetic aspects. Electrophoresis 9:681–692
Granvogl B, Reisinger V, Eichacker LA (2006) Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains. Proteomics 6:3681–3695
Gross JH (2011) Mass spectrometry: a textbook. Springer, Berlin
Hägglund P, Bunkenborg J, Maeda K, Svensson B (2008) Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags. J Proteome Res 7:5270–5276
Hägglund P, Bunkenborg J, Yang F, Harder LM, Finnie C, Svensson B (2010) Identification of thioredoxin target disulfides in proteins released from barley aleurone layers. J Proteomics 73:1133–1136
Hägglund P, Bjornberg O, Navrot N, Jensen JM, Maeda K, Kirkensgaard K, Shahpiri A, Sultan A, Bunkenborg J, Gubler F, Barrero JM, Henriksen A, Finnie C, Svensson B (2013) The barley grain thioredoxin system—an update. Front Plant Sci. https://doi.org/10.3389/fpls.2013.00151
Hägglund P, Finnie C, Yano H, Shahpiri A, Buchanan BB, Henriksen A, Svensson B (2016) Seed thioredoxin h. Biochim Biophys Acta-Proteins Proteomics 1864:974–982
Hooper CM, Castleden IR, Aryamanesh N, Jacoby RP, Millar AH (2016) Finding the subcellular location of barley, wheat, rice and maize proteins: the compendium of crop proteins with annotated locations (cropPAL). Plant Cell Physiol 57
Hurkman WJ, Tanaka CK (1986) Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis. Plant Physiol 81:802–806
Hynek R, Svensson B, Jensen ON, Barkholt V, Finnie C (2006) Enrichment and identification of integral membrane proteins from barley aleurone layers by reversed-phase chromatography, SDS-PAGE, and LC-MS/MS. J Proteome Res 5:3105–3113
Hynek R, Svensson B, Jensen ON, Barkholt V, Finnie C (2009) The plasma membrane proteome of germinating barley embryos. Proteomics 9:3787–3794
Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17:388–391
Johnova P, Skalak J, Saiz-Fernandez I, Brzobohaty B (2016) Plant responses to ambient temperature fluctuations and water-limiting conditions: a proteome-wide perspective. Biochim Biophys Acta-Proteins Proteomics 1864:916–931
Kaspar S, Matros A, Mock HP (2010a) Proteome and flavonoid analysis reveals distinct responses of epidermal tissue and whole leaves upon UV-B radiation of barley (Hordeum vulgare L.) seedlings. J Proteome Res 9:2402–2411
Kaspar S, Weier D, Weschke W, Mock HP, Matros A (2010b) Protein analysis of laser capture micro-dissected tissues revealed cell-type specific biological functions in developing barley grains. Anal Bioanal Chem 398:2883–2893
Kaspar-Schoenefeld S, Merx K, Jozefowicz AM, Hartmann A, Seiffert U, Weschke W, Matros A, Mock HP (2016) Label-free proteome profiling reveals developmental-dependent patterns in young barley grains. J Proteomics 143:106–121
Kausar R, Arshad M, Shahzad A, Komatsu S (2013) Proteomics analysis of sensitive and tolerant barley genotypes under drought stress. Amino Acids 44:345–359
Kosova K, Vitamvas P, Prasil IT (2014) Proteomics of stress responses in wheat and barley-search for potential protein markers of stress tolerance. Front Plant Sci. https://doi.org/10.3389/fpls.2014.00711
Kosova K, Vitamvas P, Urban MO, Klima M, Roy A, Prasil IT (2015) Biological networks underlying abiotic stress tolerance in temperate crops-a proteomic perspective. Int J Mol Sci 16:20913–20942
Lastovickova M, Bobalova J (2012) MS based proteomic approaches for analysis of barley malt. J Cereal Sci 56:519–530
Lozano RM, Wong JH, Yee BC, Peters A, Kobrehel K, Buchanan BB (1996) New evidence for a role for thioredoxin h in germination and seedling development. Planta 200:100–106
Maeda K, Finnie C, Ostergaard O, Svensson B (2003) Identification, cloning and characterization of two thioredoxin H isoforms, HvTrxh1 and HvTrxh2, from the barley seed proteome. Eur J Biochem 270:2633–2643
Maeda K, Finnie C, Svensson B (2004) Cy5 maleimide labelling for sensitive detection of free thiols in native protein extracts: identification of seed proteins targeted by barley thioredoxin h isoforms. Biochem J 378:497–507
Mahalingam R (2017) Shotgun proteomics of the barley seed proteome. Bmc Genomics 18
March TJ, Richter D, Colby T, Harzen A, Schmidt J, Pillen K (2012) Identification of proteins associated with malting quality in a subset of wild barley introgression lines. Proteomics 12:2843–2851
Marsalova L, Vitamvas P, Hynek R, Prasil IT, Kosova K (2016) Proteomic response of Hordeum vulgare cv. Tadmor and Hordeum marinum to salinity stress: similarities and differences between a glycophyte and a halophyte. Front Plant Sci. https://doi.org/10.3389/fpls.2016.01154
Marx C, Wong JH, Buchanan BB (2003) Thioredoxin and germinating barley: targets and protein redox changes. Planta 216:454–460
Matros A, Kaspar S, Witzel K, Mock HP (2011) Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. Phytochemistry 72:963–974
Moller ALB, Pedas P, Andersen B, Svensson B, Schjoerring JK, Finnie C (2011) Responses of barley root and shoot proteomes to long-term nitrogen deficiency, short-term nitrogen starvation and ammonium. Plant, Cell Environ 34:2024–2037
Mustafa G, Komatsu S (2016) Toxicity of heavy metals and metal-containing nanoparticles on plants. Biochim Biophys Acta-Proteins Proteomics 1864:932–944
Nelson CJ, Alexova R, Jacoby RP, Millar AH (2014) Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling. Plant Physiol 166:91–108
Osinalde N, Aloria K, Omaetxebarria MJ, Kratchmarova I (2017) Targeted mass spectrometry: an emerging powerful approach to unblock the bottleneck in phosphoproteomics. J Chromatogr B-Anal Technol Biomed Life Sci 1055:29–38
Ostergaard O, Finnie C, Laugesen S, Roepstorff P, Svensson B (2004) Proteome analysis of barley seeds: identification of major proteins from two-dimensional gels (pl 4-7). Proteomics 4:2437–2447
Patton WF (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21:1123–1144
Pennington HG, Gheorghe DM, Damerum A, Pliego C, Spanu PD, Cramer R, Bindschedler LV (2016) Interactions between the powdery mildew effector BEC1054 and barley proteins identify candidate host targets. J Proteome Res 15:826–839
Perrocheau L, Rogniaux H, Boivin P, Marion D (2005) Probing heat-stable water-soluble proteins from barley to malt and beer. Proteomics 5:2849–2858
Petersen J, Rogowska-Wrzesinska A, Jensen ON (2013) Functional proteomics of barley and barley chloroplasts—strategies, methods and perspectives. Front Plant Sci. https://doi.org/10.3389/fpls.2013.00052
Picotti P, Aebersold R (2012) Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods 9:555–566
Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138:795–806
Ploscher M, Granvogl B, Zoryan M, Reisinger V, Eichacker LA (2009) Mass spectrometric characterization of membrane integral low molecular weight proteins from photosystem II in barley etioplasts. Proteomics 9:625–635
Ploscher M, Reisinger V, Eichacker LA (2011) Proteomic comparison of etioplast and chloroplast protein complexes. J Proteomics 74:1256–1265
Pos V, Hunyadi-Gulyas E, Caiazzo R, Jocsak I, Medzihradszky KF, Lukacs N (2011) Induction of pathogenesis-related proteins in intercellular fluid by cadmium stress in barley (Hordeum vulgare L.)—a proteomic analysis. Acta Aliment 40:164–175
Rasoulnia A, Bihamta MR, Peyghambari SA, Alizadeh H, Rahnama A (2011) Proteomic response of barley leaves to salinity. Mol Biol Rep 38:5055–5063
Rollins JA, Habte E, Templer SE, Colby T, Schmidt J, von Korff M (2013) Leaf proteome alterations in the context of physiological and morphological responses to drought and heat stress in barley (Hordeum vulgare L.). J Exp Bot 64:3201–3212
Schneider T, Schellenberg M, Meyer S, Keller F, Gehrig P, Riedel K, Lee Y, Eberl L, Martinoia E (2009) Quantitative detection of changes in the leaf-mesophyll tonoplast proteome in dependency of a cadmium exposure of barley (Hordeum vulgare L.) plants. Proteomics 9:2668–2677
Sharma SS, Dietz KJ, Mimura T (2016) Vacuolar compartmentalization as indispensable component of heavy metal detoxification in plants. Plant, Cell Environ 39:1112–1126
Shen JR (2015) The structure of photosystem II and the mechanism of water oxidation in photosynthesis. In Merchant SS (ed) Annual review of plant biology, vol 66, pp 23–48
Shen QF, Fu LB, Dai F, Jiang LX, Zhang GP, Wu DZ (2016) Multi-omics analysis reveals molecular mechanisms of shoot adaption to salt stress in Tibetan wild barley. Bmc Genomics 17
Shen QF, Fu LB, Qiu L, Xue F, Zhang GP, Wu DZ (2017) Time-course of ionic responses and proteomic analysis of a Tibetan wild barley at early stage under salt stress. Plant Growth Regul 81:11–21
Shevela D, Arnold J, Reisinger V, Berends HM, Kmiec K, Koroidov S, Bue AK, Messinger J, Eichacker LA (2016) Biogenesis of water splitting by photosystem II during de-etiolation of barley (Hordeum vulgare L.). Plant, Cell Environ 39:1524–1536
Sreenivasulu N, Borisjuk L, Junker BH, Mock HP, Rolletschek H, Seiffert U, Weschke W, Wobus U (2010) Barley grain development: toward an integrative view. Int Rev Cell Mol Biol 281:49–89
Sultan A, Andersen B, Svensson B, Finnie C (2016) Exploring the plant-microbe interface by profiling the surface-associated proteins of barley grains. J Proteome Res 15:1151–1167
Tanaka K (2003) The origin of macromolecule ionization by laser irradiation (Nobel lecture). Angew Chem (International Edition) 42:3860–3870
Trumper C, Paffenholz K, Smit I, Kossler P, Karlovsky P, Braun HP, Pawelzik E (2016) Identification of regulated proteins in naked barley grains (Hordeum vulgare nudum) after Fusarium graminearum infection at different grain ripening stages. J Proteomics 133:86–92
Wang XL, Cai XF, Xu CX, Wang QH, Dai SJ (2016) Drought-responsive mechanisms in plant leaves revealed by proteomics. Int J Mol Sci 17
Weiss W, Postel W, Gorg A (1991) Barley cultivar discrimination. 2. Sodium dodecyl sulfate-Polyacrylamide gel-electrophoresis and isoelectric-focusing with immobilized pH gradients. Electrophoresis 12:330–337
Wendelboe-Nelson C, Morris PC (2012) Proteins linked to drought tolerance revealed by DIGE analysis of drought resistant and susceptible barley varieties. Proteomics 12:3374–3385
Witzel K, Mock H-P (2016) A proteomic view of the cereal and vegetable crop response to salinity stress. In: Agricultural proteomics, vol 2. Springer, Berlin, pp 53–69
Witzel K, Weidner A, Surabhi GK, Borner A, Mock HP (2009) Salt stress-induced alterations in the root proteome of barley genotypes with contrasting response towards salinity. J Exp Bot 60:3545–3557
Witzel K, Weidner A, Surabhi GK, Varshney RK, Kunze G, Buck-Sorlin GH, Borner A, Mock HP (2010) Comparative analysis of the grain proteome fraction in barley genotypes with contrasting salinity tolerance during germination. Plant, Cell Environ 33:211–222
Witzel K, Pietsch C, Strickert M, Matros A, Roder M, Weschke W, Wobus U, Mock HP (2011) Mapping of quantitative trait loci associated with protein expression variation in barley grains. Mol Breeding 27:301–314
Witzel K, Matros A, Strickert M, Kaspar S, Peukert M, Mühling KH, Börner A, Mock H-P (2014) Salinity stress in roots of contrasting barley genotypes reveals time-distinct and genotype-specific patterns for defined proteins. Mol Plant 7:336–355
Wu D, Shen Q, Qiu L, Han Y, Ye L, Jabeen Z, Shu Q, Zhang G (2014) Identification of proteins associated with ion homeostasis and salt tolerance in barley. Proteomics 14:1381–1392
Yang F, Jensen JD, Spliid NH, Svensson B, Jacobsen S, Jorgensen LN, Jorgensen HJL, Collinge DB, Finnie C (2010a) Investigation of the effect of nitrogen on severity of Fusarium Head Blight in barley. J Proteomics 73:743–752
Yang F, Jensen JD, Svensson B, Jorgensen HJL, Collinge DB, Finnie C (2010b) Analysis of early events in the interaction between Fusarium graminearum and the susceptible barley (Hordeum vulgare) cultivar Scarlett. Proteomics 10:3748–3755
Zeng ZX, Jiang JM (2016) Isolation and proteomics analysis of barley centromeric chromatin using PICh. J Proteome Res 15:1875–1882
Zolla L, Rinalducci S, Timperio AM, Huber CG (2002) Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatography-electrospray ionization mass spectrometry. Photosystem I. Plant Physiology 130:1938–1950
Acknowledgements
The authors wish to thank many funding agencies for support of their proteomic research. H. -P. Mock wishes to thank the German Science Foundation DFG, the BMBF and the BMEL as well as the DAAD. BS wishes to thank the Carlsberg Foundation, and the Danish Council for Independent Research|Natural Sciences and Technical and Production Sciences. CF wishes to thank the Danish Council for Independent Research|Natural Sciences and the Novo Nordisk Foundation. We also wish to thank two anonymous reviewers for valuable suggestions.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Mock, HP., Finnie, C., Witzel, K., Svensson, B. (2018). Barley Proteomics. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_19
Download citation
DOI: https://doi.org/10.1007/978-3-319-92528-8_19
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-92527-1
Online ISBN: 978-3-319-92528-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)