Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring.

Abstract:

:Although the economic value of wheat flour is determined by the complement of gluten proteins, these proteins have been challenging to study because of the complexity of the major protein groups and the tremendous sequence diversity among wheat cultivars. The completion of a high-quality wheat genome sequence from the reference wheat Chinese Spring recently facilitated the assembly and annotation of a complete set of gluten protein genes from a single cultivar, making it possible to link individual proteins in the flour to specific gene sequences. In a proteomic analysis of total wheat flour protein from Chinese Spring using quantitative two-dimensional gel electrophoresis combined with tandem mass spectrometry, gliadins or low-molecular-weight glutenin subunits were identified as the predominant proteins in 72 protein spots. Individual spots were associated with 40 of 56 Chinese Spring gene sequences, including 16 of 26 alpha gliadins, 10 of 11 gamma gliadins, six of seven omega gliadins, one of two delta gliadins, and nine of ten LMW-GS. Most genes that were not associated with protein spots were either expressed at low levels in endosperm or encoded proteins with high similarity to other proteins. A wide range of protein accumulation levels were observed and discrepancies between transcript levels and protein levels were noted. This work together with similar studies using other commercial cultivars should provide new insight into the molecular basis of wheat flour quality and allergenic potential.

journal_name

Funct Integr Genomics

authors

Altenbach SB,Chang HC,Simon-Buss A,Mohr T,Huo N,Gu YQ

doi

10.1007/s10142-019-00694-z

subject

Has Abstract

pub_date

2020-01-01 00:00:00

pages

1-16

issue

1

eissn

1438-793X

issn

1438-7948

pii

10.1007/s10142-019-00694-z

journal_volume

20

pub_type

杂志文章
  • Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids.

    abstract::The symbiotic N(2)-fixing alpha-proteobacterium Sinorhizobium meliloti has three replicons: a circular chromosome (3.7 Mb) and two smaller replicons, pSymA (1.4 Mb) and pSymB (1.7 Mb). Sequence analysis has revealed that an essential gene is carried on pSymB, which brings into question whether pSymB should be consider...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-002-0068-0

    authors: Wong K,Finan TM,Golding GB

    更新日期:2002-11-01 00:00:00

  • Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley.

    abstract::Barley (Hordeum vulgare L.) is one of the most important large-genome cereals with extensive genetic resources available in the public sector. Studies of genome organization in barley have been limited primarily to genetic markers and sparse sequence data. Here we report sequence analysis of 417.5 kb DNA from four BAC...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-002-0055-5

    authors: Rostoks N,Park YJ,Ramakrishna W,Ma J,Druka A,Shiloff BA,SanMiguel PJ,Jiang Z,Brueggeman R,Sandhu D,Gill K,Bennetzen JL,Kleinhofs A

    更新日期:2002-05-01 00:00:00

  • Gene therapy--when a simple concept meets a complex reality. Review on gene therapy.

    abstract::In theory, gene therapy is a simple concept which holds great promise as a cure for disease. In practice, however, considerable obstacles have to be overcome, including problems with safe and efficient gene delivery and stable gene expression. This review gives an overview on the history of gene therapy and analyses s...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s101420000011

    authors: Grosshans H

    更新日期:2000-09-01 00:00:00

  • GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis.

    abstract::In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergenc...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-018-0605-0

    authors: Upadhyay A,Maske S,Jogaiah S,Kadoo NY,Gupta VS

    更新日期:2018-07-01 00:00:00

  • Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau.

    abstract::Natural selection drives species adaptations to biotic and abiotic stresses. Species distributed along a moisture gradient, such as Stipa purpurea, a dominant grass in alpine arid and semi-arid meadows on the Tibetan Plateau, provide an opportunity to evaluate the effects of long-term adaptation to differing degrees o...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-014-0419-7

    authors: Yang Y,Li X,Kong X,Ma L,Hu X,Yang Y

    更新日期:2015-05-01 00:00:00

  • Transactivation of a target gene through feedforward loop activation in plants.

    abstract::The expression of many genes encoding transcriptional activators in prokaryotes and eukaryotes is upregulated through positive feedback activation. During positive feedback activation, a transcriptional activator binds to its own promoter and thus increases its own expression as well as the expression of its target ge...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s101420000001

    authors: Schwechheimer C,Corke FM,Smith CH,Bevan M

    更新日期:2000-05-01 00:00:00

  • Functional features of a single chromosome arm in wheat (1AL) determined from its structure.

    abstract::Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so ...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-011-0250-3

    authors: Lucas SJ,Šimková H,Šafář J,Jurman I,Cattonaro F,Vautrin S,Bellec A,Berges H,Doležel J,Budak H

    更新日期:2012-03-01 00:00:00

  • Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects.

    abstract::We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-020-00757-6

    authors: Emisoglu-Kulahli H,Gul S,Morgil H,Ozcan O,Aygenli F,Selvi S,Kavakli IH,Ozturk N

    更新日期:2021-01-01 00:00:00

  • Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii.

    abstract::Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In thi...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-015-0437-0

    authors: Sun R,Wang K,Guo T,Jones DC,Cobb J,Zhang B,Wang Q

    更新日期:2015-07-01 00:00:00

  • Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers.

    abstract::EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs ((SSR)ESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl scrip...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-004-0128-8

    authors: Peng JH,Lapitan NL

    更新日期:2005-04-01 00:00:00

  • Genome-wide analysis of water-stress-responsive microRNA expression profile in tobacco roots.

    abstract::MicroRNAs (miRNAs) play a pivotal role in post-transcriptional regulation of gene expression in plants. In this study, we investigate miRNAs in an agronomically important common tobacco in China, named Honghua Dajinyuan (a drought-tolerant cultivar). Here, we report a comprehensive analysis of miRNA expression profile...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-014-0365-4

    authors: Yin F,Gao J,Liu M,Qin C,Zhang W,Yang A,Xia M,Zhang Z,Shen Y,Lin H,Luo C,Pan G

    更新日期:2014-06-01 00:00:00

  • Identification and characterization of microRNAs in the plant parasitic root-knot nematode Meloidogyne incognita using deep sequencing.

    abstract::The root-knot nematode Meloidogyne incognita is among the most damaging plant-parasitic pests of several crops including cotton (Gossypium hirsutum) and tomato (Lycopersicon escultentum). Recently, a genome has become available for M. incognita, which greatly facilitates investigation of the interactions between M. in...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-015-0472-x

    authors: Zhang Y,Wang Y,Xie F,Li C,Zhang B,Nichols RL,Pan X

    更新日期:2016-03-01 00:00:00

  • Conserved synteny-based anchoring of the barley genome physical map.

    abstract::Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene l...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-013-0327-2

    authors: Poursarebani N,Ariyadasa R,Zhou R,Schulte D,Steuernagel B,Martis MM,Graner A,Schweizer P,Scholz U,Mayer K,Stein N

    更新日期:2013-08-01 00:00:00

  • A novel alkyl hydroperoxidase (AhpD) of Anabaena PCC7120 confers abiotic stress tolerance in Escherichia coli.

    abstract::In silico analysis together with cloning, molecular characterization and heterologous expression reports that the hypothetical protein All5371 of Anabaena sp. PCC7120 is a novel hydroperoxide scavenging protein similar to AhpD of bacteria. The presence of E(X)11CX HC(X)3H motif in All5371 confers peroxidase activity a...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-014-0407-y

    authors: Shrivastava AK,Singh S,Singh PK,Pandey S,Rai LC

    更新日期:2015-01-01 00:00:00

  • Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection.

    abstract::Gastrointestinal nematodes of the genus Cooperia are arguably the most important parasites of cattle. The bovine jejunal transcriptome was characterized in response to Cooperia oncophora infection using RNA-seq technology. Approximately 71% of the 25,670 bovine genes were detected in the jejunal transcriptome. However...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-011-0259-7

    authors: Li RW,Schroeder SG

    更新日期:2012-03-01 00:00:00

  • Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes.

    abstract::GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress respo...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-018-0620-1

    authors: Cao Y,Han Y,Meng D,Abdullah M,Yu J,Li D,Jin Q,Lin Y,Cai Y

    更新日期:2018-11-01 00:00:00

  • Analysis of miRNA-seq in the liver of common carp (Cyprinus carpio L.) in response to different environmental temperatures.

    abstract::Water temperature affects the survival, growth, immunity, reproduction, and productivity of farmed fish. The temperature beyond suitable range will disrupt the normal physiological activity. Common carp (Cyprinus carpio L.) is a representative eurythermic fish; they are able to sense and respond to changes in water te...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-018-0643-7

    authors: Sun J,Zhao L,Wu H,Lian W,Cui C,Du Z,Luo W,Li M,Yang S

    更新日期:2019-03-01 00:00:00

  • Gene networks in the synthesis and deposition of protein polymers during grain development of wheat.

    abstract::As the amino acid storing organelle, the protein bodies provide nutrients for embryo development, seed germination and early seedling growth through storage proteolysis in cereal plants, such as wheat and rice. In protein bodies, the monomeric and polymeric prolamins, i.e. gliadins and glutenins, form gluten and play ...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-010-0196-x

    authors: She M,Ye X,Yan Y,Howit C,Belgard M,Ma W

    更新日期:2011-03-01 00:00:00

  • Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle.

    abstract::Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes. In this study, we performed a large-scale analysis o...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-011-0252-1

    authors: Hou Y,Liu GE,Bickhart DM,Matukumalli LK,Li C,Song J,Gasbarre LC,Van Tassell CP,Sonstegard TS

    更新日期:2012-03-01 00:00:00

  • Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice.

    abstract::Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-012-0274-3

    authors: Sharma R,Agarwal P,Ray S,Deveshwar P,Sharma P,Sharma N,Nijhawan A,Jain M,Singh AK,Singh VP,Khurana JP,Tyagi AK,Kapoor S

    更新日期:2012-06-01 00:00:00

  • Major intrinsic proteins (MIPs) in plants: a complex gene family with major impacts on plant phenotype.

    abstract::The ubiquitous cell membrane proteins called aquaporins are now firmly established as channel proteins that control the specific transport of water molecules across cell membranes in all living organisms. The aquaporins are thus likely to be of fundamental significance to all facets of plant growth and development aff...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-007-0049-4

    authors: Forrest KL,Bhave M

    更新日期:2007-10-01 00:00:00

  • Chromosomes in the flow to simplify genome analysis.

    abstract::Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be ...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-012-0293-0

    authors: Doležel J,Vrána J,Safář J,Bartoš J,Kubaláková M,Simková H

    更新日期:2012-08-01 00:00:00

  • Transcriptomic profiling of developing fiber in levant cotton (Gossypium herbaceum L.).

    abstract::Cotton (Gossypium spp.) is an imperative economic crop of the globe due to its natural textile fiber. Molecular mechanisms of fiber development have been greatly revealed in allotetraploid cotton but remained unexplored in Gossypium herbaceum. G. herbaceum can withstand the rigors of nature like drought and pests but ...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-017-0586-4

    authors: Parekh MJ,Kumar S,Fougat RS,Zala HN,Pandit RJ

    更新日期:2018-03-01 00:00:00

  • Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress.

    abstract::Medicago sativa L. (alfalfa) 'Zhaodong' is an important forage legume that can safely survive in northern China where winter temperatures reach as low as -30 °C. Survival of alfalfa following freezing stress depends on the amount and revival ability of crown buds. In order to investigate the molecular mechanisms of fr...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-016-0500-5

    authors: Song L,Jiang L,Chen Y,Shu Y,Bai Y,Guo C

    更新日期:2016-09-01 00:00:00

  • The entangled history of animal and plant microRNAs.

    abstract::MicroRNAs (miRNAs) are small RNAs (sRNAs) that regulate gene expression in development and adaptive responses to the environment. The early days in the sRNA field was one of the most exciting and promising moments in modern biology, attracting large investments to the understanding of the underlining mechanisms and th...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-016-0513-0

    authors: Reis RS

    更新日期:2017-05-01 00:00:00

  • Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus.

    abstract::Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes s...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-020-00735-y

    authors: Li X,Li C,Xu Y,Yao R,Li H,Ni W,Quan R,Zhang M,Liu L,Yu S,Ullah Y,Hu R,Li Y,Guo T,Wang X,Hu S

    更新日期:2020-07-01 00:00:00

  • QTLian breeding for climate resilience in cereals: progress and prospects.

    abstract::The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consume...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-019-00684-1

    authors: Choudhary M,Wani SH,Kumar P,Bagaria PK,Rakshit S,Roorkiwal M,Varshney RK

    更新日期:2019-09-01 00:00:00

  • Differential expression of peroxidase and ABC transporter as the key regulatory components for degradation of azo dyes by Penicillium oxalicum SAR-3.

    abstract::Fungal species are potential dye decomposers since these secrete spectra of extracellular enzymes involved in catabolism. However, cellular mechanisms underlying azo dye catalysis and detoxification are incompletely understood and obscure. A potential strain designated as Penicillium oxalicum SAR-3 demonstrated broad-...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-014-0405-0

    authors: Saroj S,Kumar K,Prasad M,Singh RP

    更新日期:2014-12-01 00:00:00

  • The bioinformatics challenges in comparative analysis of cereal genomes-an overview.

    abstract::Comparative genomic analysis is the cornerstone of in silico-based approaches to understanding biological systems and processes across cereal species, such as rice, wheat and barley, in order to identify genes of agronomic interest. The size of the genomic repositories is nearly doubling every year, and this has signi...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章,评审

    doi:10.1007/s10142-004-0102-5

    authors: Bellgard M,Ye J,Gojobori T,Appels R

    更新日期:2004-03-01 00:00:00

  • Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage.

    abstract::The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC librar...

    journal_title:Functional & integrative genomics

    pub_type: 杂志文章

    doi:10.1007/s10142-011-0237-0

    authors: Zhang J,Jia J,Breen J,Kong X

    更新日期:2011-12-01 00:00:00