Genomes and Genes
Summary: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
- Gusberti M, Gessler C, Broggini G. RNA-Seq analysis reveals candidate genes for ontogenic resistance in Malus-Venturia pathosystem. PLoS ONE. 2013;8:e78457 pubmed publisher..The modulation of the five candidate genes has been validated using the real-time quantitative PCR. Thus, ontogenic resistance may be the result of the corresponding up- and down-regulation of these genes. ..
- Wong C, Singh M, Bhalla P. The dynamics of soybean leaf and shoot apical meristem transcriptome undergoing floral initiation process. PLoS ONE. 2013;8:e65319 pubmed publisher..Further, evidence is emerging that the conversion of shoot apical meristem to inflorescence meristem is linked with the interplay of auxin, cytokinin and GA creating a low cytokinin and high GA environment...
- Ecker C, Ertl A, Pulverer W, Nemes A, Szekely P, Petrasch A, et al. Validation and comparison of a sandwich ELISA, two competitive ELISAs and a real-time PCR method for the detection of lupine in food. Food Chem. 2013;141:407-18 pubmed publisher..In addition, the methods were applied to the analysis of commercial foodstuffs differing in their labelling. ..
- Léran S, Varala K, Boyer J, Chiurazzi M, Crawford N, Daniel Vedele F, et al. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. Trends Plant Sci. 2014;19:5-9 pubmed publisher..In comparison to their animal and bacterial counterparts, these plant proteins transport a wide variety of substrates: nitrate, peptides, amino acids, dicarboxylates, glucosinolates, IAA, ..
- Oda T, Kikkawa M. Novel structural labeling method using cryo-electron tomography and biotin-streptavidin system. J Struct Biol. 2013;183:305-311 pubmed publisher..In conclusion, the combination of the biotin-streptavidin system and cryo-electron tomography is a powerful method to investigate the structure of large macromolecular complexes. ..
- Hurlburt B, Offermann L, McBride J, Majorek K, Maleki S, Chruszcz M. Structure and function of the peanut panallergen Ara h 8. J Biol Chem. 2013;288:36890-901 pubmed publisher..The overall fold is very similar to that of Bet v 1, Api g 1 (celery), Gly m 4 (soy), and Pru av 1 (cherry). Ara h 8 binds the isoflavones quercetin and apigenin as well as resveratrol avidly. ..
- Zhang X, Rerksiri W, Liu A, Zhou X, Xiong H, Xiang J, et al. Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf. Gene. 2013;530:185-92 pubmed publisher..The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement. ..
- Nakamura H, Xue Y, Miyakawa T, Hou F, Qin H, Fukui K, et al. Molecular mechanism of strigolactone perception by DWARF14. Nat Commun. 2013;4:2613 pubmed publisher..The D14 residues recognizing D-OH are critical for the SL-dependent D14-SLR1 interaction. These results provide new insight into crosstalk between gibberellin and SL signalling pathways. ..
- Cakir B, Kılıçkaya O. Whole-genome survey of the putative ATP-binding cassette transporter family genes in Vitis vinifera. PLoS ONE. 2013;8:e78860 pubmed publisher..This inventory could help elucidate the biological and physiological functions of these transporters in V. vinifera. ..
- Yin Z, Wang J, Wang D, Fan W, Wang S, Ye W. The MAPKKK gene family in Gossypium raimondii: genome-wide identification, classification and expression analysis. Int J Mol Sci. 2013;14:18740-57 pubmed publisher..Twelve MAPKKK genes were more highly expressed in 3-DPA ovules than in 0-DPA ovules. Our results provide a foundation for future evolutionary and functional characterizations of MAPKKK genes in cotton and probably other Gossypium plants...
- Monshausen G, Haswell E. A force of nature: molecular mechanisms of mechanoperception in plants. J Exp Bot. 2013;64:4663-80 pubmed publisher..We also discuss how the secondary messenger Ca(2+) operates at the centre of many of these mechanical signal transduction pathways. ..
- Liu H, Charng Y. Common and distinct functions of Arabidopsis class A1 and A2 heat shock factors in diverse abiotic stress responses and development. Plant Physiol. 2013;163:276-90 pubmed publisher..Overall, this study reveals the overlapping and distinct functions of class A1 and A2 HSFs and may enable more precise use of HSFs in engineering stress tolerance in the future. ..
- Dong S, Stam R, Cano L, Song J, Sklenar J, Yoshida K, et al. Effector specialization in a lineage of the Irish potato famine pathogen. Science. 2014;343:552-5 pubmed publisher..Amino acid polymorphisms in both the inhibitors and their target proteases underpin this biochemical specialization. Our results link effector specialization to diversification and speciation of this plant pathogen. ..
- Lu S, Li Q, Wei H, Chang M, Tunlaya Anukit S, Kim H, et al. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc Natl Acad Sci U S A. 2013;110:10848-53 pubmed publisher..Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content. ..
- Jin J, Zhang H, Kong L, Gao G, Luo J. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res. 2014;42:D1182-7 pubmed publisher..In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences. ..
- Hedman H, Zhu T, von Arnold S, Sohlberg J. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in the conifer picea abies reveals extensive conservation as well as dynamic patterns. BMC Plant Biol. 2013;13:89 pubmed publisher..Most studies have examined the function of these genes in angiosperms and very little is known from other plant species...
- Chen L, Zhou X, Li W, Chang W, Zhou R, Wang C, et al. Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions. BMC Genomics. 2013;14:687 pubmed publisher..Using Digital Gene Expression Tag profiling (DGE), a new technique based on Illumina sequencing, we analyzed expression profiles between two soybean genotypes to identify drought-responsive genes...
- Chakrabarti M, Zhang N, Sauvage C, Muños S, Blanca J, Canizares J, et al. A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci U S A. 2013;110:17125-30 pubmed publisher..Altogether, our findings shed light on the molecular basis of fruit mass, a key domestication trait in tomato and other fruit and vegetable crops. ..
- Yokotani N, Sato Y, Tanabe S, Chujo T, Shimizu T, Okada K, et al. WRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance. J Exp Bot. 2013;64:5085-97 pubmed publisher..These results strongly suggest that OsWRKY76 plays dual and opposing roles in blast disease resistance and cold tolerance. ..
- Zhou G, Delhaize E, Zhou M, Ryan P. The barley MATE gene, HvAACT1, increases citrate efflux and Al(3+) tolerance when expressed in wheat and barley. Ann Bot. 2013;112:603-12 pubmed publisher..The aim of this study was to investigate whether expressing HvAACT1 with a constitutive promoter in barley and wheat can increase citrate efflux and Al(3+) tolerance of these important cereal species...
- Plazas M, López Gresa M, Vilanova S, Torres C, Hurtado M, Gramazio P, et al. Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning. J Agric Food Chem. 2013;61:8871-9 pubmed publisher..Results suggest that it is possible to develop new eggplant varieties with improved functional and apparent quality. ..
- Meng X, Chen Q, Fan H, Song T, Cui N, Zhao J, et al. Molecular characterization, expression analysis and heterologous expression of two translationally controlled tumor protein genes from Cucumis sativus. PLoS ONE. 2017;12:e0184872 pubmed publisher..In a prokaryotic expression analysis, CsTCTP1 and CsTCTP2 showed positive responses to salt and heat stresses and a negative response to drought and HgCl2 stresses. TCTP may exert multiple functions in various cellular processes...
- Karasinski J, Wrobel K, Corrales Escobosa A, Konopka A, Bulska E, Wrobel K. Allium cepa L. Response to Sodium Selenite (Se(IV)) Studied in Plant Roots by a LC-MS-Based Proteomic Approach. J Agric Food Chem. 2017;65:3995-4004 pubmed publisher..cepa L., potentially limiting accumulation of Se in the form of nonprotein methylated species and affecting adversely transmethylation-dependent signaling pathways. ..
- Ziems L, Hickey L, Platz G, Franckowiak J, Dracatos P, Singh D, et al. Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley. Phytopathology. 2017;107:834-841 pubmed publisher..Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection. ..
- Ahmad J, Bashir H, Bagheri R, Baig A, Al Huqail A, Ibrahim M, et al. Drought and salinity induced changes in ecophysiology and proteomic profile of Parthenium hysterophorus. PLoS ONE. 2017;12:e0185118 pubmed publisher..Proteins involved in molecular stabilization, formation of osmolytes and wax and contributing to stress-avoiding anatomical features emerged as key and complex mechanisms for imparting stress tolerance to P. hysterophorus. ..
- Wei Y, Zhou D, Peng J, Pan L, Tu K. Hot Air Treatment Induces Disease Resistance through Activating the Phenylpropanoid Metabolism in Cherry Tomato Fruit. J Agric Food Chem. 2017;65:8003-8010 pubmed publisher..The results suggest that HA treatment induces disease resistance by activating the phenylpropanoid pathway in cherry tomato fruit. ..
- Healey R, Lebhar H, Hornung S, Thordarson P, Marquis C. An improved process for the production of highly purified recombinant thaumatin tagged-variants. Food Chem. 2017;237:825-832 pubmed publisher..These new thaumatin variants are amenable for bioconjugation, providing chemical biology tools for thaumatin:taste receptor interaction studies. ..
- Qin R, Zeng D, Liang R, Yang C, Akhter D, Alamin M, et al. Rice gene SDL/RNRS1, encoding the small subunit of ribonucleotide reductase, is required for chlorophyll synthesis and plant growth development. Gene. 2017;627:351-362 pubmed publisher..The "SDL/RNRS1" was, hence, required for the chlorophyll biosynthesis and also played pleiotropic roles in the regulation of plant development. ..
- Wang X, Appels R, Zhang X, Diepeveen D, Török K, Tomoskozi S, et al. Protein interactions during flour mixing using wheat flour with altered starch. Food Chem. 2017;231:247-257 pubmed publisher..The findings provide new entry points for modifying final product attributes. ..
- Naing A, Park K, Ai T, Chung M, Han J, Kang Y, et al. Overexpression of snapdragon Delila (Del) gene in tobacco enhances anthocyanin accumulation and abiotic stress tolerance. BMC Plant Biol. 2017;17:65 pubmed publisher..The resultant increase of anthocyanin and antioxidant activity improves abiotic stress tolerance. ..
- Dzidzienyo D, Bryan G, Wilde G, Robbins T. Allelic diversity of S-RNase alleles in diploid potato species. Theor Appl Genet. 2016;129:1985-2001 pubmed publisher..The progeny analysis of four semi-compatible crosses examined by allele-specific PCR provided further confirmation that these are functional S-RNases. ..
- Liu W, Wang Y, Zhang Z, Wang M, Lv Q, Liu H, et al. Generation and characterization of caprine chymosin in corn seed. Protein Expr Purif. 2017;135:78-82 pubmed publisher..5 U/mg. These results indicate that we have successfully established a technology for generating corn seed-derived caprine chymosin for potential use in the dairy industry. ..
- Panozzo S, Milani A, Scarabel L, Balogh Á, Dancza I, Sattin M. Occurrence of Different Resistance Mechanisms to Acetolactate Synthase Inhibitors in European Sorghum halepense. J Agric Food Chem. 2017;65:7320-7327 pubmed publisher..halepense. ALS enzyme bioassay and treatment with malathion confirmed that at least in plants of two populations the resistance is very likely due to both target-site and enhanced metabolism of P450 enzymes. ..
- Zhao G, Song Y, Wang C, Butt H, Wang Q, Zhang C, et al. Genome-wide identification and functional analysis of the TIFY gene family in response to drought in cotton. Mol Genet Genomics. 2016;291:2173-2187 pubmed..These data may form the basis of future studies regarding the relationship between drought and jasmonic acid. ..
- Rodsamran P, Sothornvit R. Physicochemical and functional properties of protein concentrate from by-product of coconut processing. Food Chem. 2018;241:364-371 pubmed publisher..Therefore, the coconut residues after extractions might be a potential alternative renewable plant protein source to use asa food ingredient to enhance food nutrition and quality. ..
- Parvathaneni R, DeLeo V, Spiekerman J, Chakraborty D, Devos K. Parallel loss of introns in the ABCB1 gene in angiosperms. BMC Evol Biol. 2017;17:238 pubmed publisher..In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss. ..
- Salojärvi J, Smolander O, Nieminen K, Rajaraman S, Safronov O, Safdari P, et al. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat Genet. 2017;49:904-912 pubmed publisher..Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A. ..
- Zaka M, Abbasi B. Effects of bimetallic nanoparticles on seed germination frequency and biochemical characterisation of Eruca sativa. IET Nanobiotechnol. 2017;11:255-260 pubmed publisher..In the authors' study, nanoparticles of small size and of high toxicity effect produced more secondary metabolites like total protein content, total flavonoids and total phenolic content. ..
- Minges A, Höppner A, Groth G. Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism. Protein Sci. 2017;26:1667-1673 pubmed publisher..Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function. ..
- Daou M, Faulds C. Glyoxal oxidases: their nature and properties. World J Microbiol Biotechnol. 2017;33:87 pubmed publisher..This aspect on GLOX remains new and needs to be investigated. ..
- Sengupta M, Raychaudhuri S. Partial alleviation of oxidative stress induced by gamma irradiation in Vigna radiata by polyamine treatment. Int J Radiat Biol. 2017;93:803-817 pubmed publisher..Expression of SAMDC also increased with putrescine treatment. This study shows that treatment with putrescine can partially alleviate oxidative damage caused by gamma rays. ..
- Luo D, Ba L, Shan W, Kuang J, Lu W, Chen J. Involvement of WRKY Transcription Factors in Abscisic-Acid-Induced Cold Tolerance of Banana Fruit. J Agric Food Chem. 2017;65:3627-3635 pubmed publisher..Taken together, our findings demonstrate that banana fruit WRKY TFs are involved in ABA-induced cold tolerance by, at least in part, increasing ABA levels via directly activating NECD expressions. ..
- Katsu K, Suzuki R, Tsuchiya W, Inagaki N, Yamazaki T, Hisano T, et al. A new buckwheat dihydroflavonol 4-reductase (DFR), with a unique substrate binding structure, has altered substrate specificity. BMC Plant Biol. 2017;17:239 pubmed publisher..The unique characteristics of FeDFR2 would provide a useful tool for future studies on the substrate specificity and organ-specific expression of DFRs. ..
- Qin J, Zhang J, Wang F, Wang J, Zheng Z, Yin C, et al. iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves. PLoS ONE. 2017;12:e0181910 pubmed publisher..This dataset will serve as the foundation for a systems biology approach to understanding photosynthetic development...
- Han X, Xu R, Duan P, Yu H, Luo Y, Li Y. Genetic analysis and identification of candidate genes for two spotted-leaf mutants (spl101 and spl102) in rice. Yi Chuan. 2017;39:346-353 pubmed publisher..In addition, our results also validate the effectiveness of the Mutmap method in cloning the candidate mutations. ..
- Morata J, PuigdomÃ¨nech P. Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes. BMC Genomics. 2017;18:138 pubmed publisher..This information could be useful both to understand the evolution of species and for plant breeding. ..
- Cuong D, Jeon J, Morgan A, Kim C, Kim J, Lee S, et al. Accumulation of Charantin and Expression of Triterpenoid Biosynthesis Genes in Bitter Melon (Momordica charantia). J Agric Food Chem. 2017;65:7240-7249 pubmed publisher..We also investigated optimum light conditions for enhancing charantin biosynthesis in bitter melon and found that red light was the most effective wavelength. ..
- Shi J, Li W, Gao Y, Wang B, Li Y, Song Z. Enhanced rutin accumulation in tobacco leaves by overexpressing the NtFLS2 gene. Biosci Biotechnol Biochem. 2017;81:1721-1725 pubmed publisher..Additionally, the transgenic tobacco plants appeared normal except for a flower color change from light red to white suggesting that it could be a valuable material for industrial extraction of rutin. ..
- Guillén Chable F, Arenas Sosa I, Islas Flores I, Corzo G, Martinez Liu C, Estrada G. Antibacterial activity and phospholipid recognition of the recombinant defensin J1-1 from Capsicum genus. Protein Expr Purif. 2017;136:45-51 pubmed publisher..Possible dimer and oligomer of HisXarJ1-1 were visible in gel electrophoresis and immunodetected with anti-His antibodies. Pure recombinant defensin HisXarJ1-1 exhibited antibacterial activity against Pseudomonas aeruginosa. ..
- Mikula K, Tascón I, Tommila J, Iwai H. Segmental isotopic labeling of a single-domain globular protein without any refolding step by an asparaginyl endopeptidase. FEBS Lett. 2017;591:1285-1294 pubmed publisher..This simple protein ligation approach using an AEP could be applied for incorporation of various biophysical probes into proteins as well as post-translational production of full-length proteins. ..
- Vulavala V, Fogelman E, Rozental L, Faigenboim A, Tanami Z, Shoseyov O, et al. Identification of genes related to skin development in potato. Plant Mol Biol. 2017;94:481-494 pubmed publisher..Cis-regulatory elements within the respective promoter sequences support this gene-expression pattern. ..
- Wang X, Zhang J, Feng X, Li H, Zhang G. The molecular mechanisms of plant plasma membrane intrinsic proteins trafficking and stress response. Yi Chuan. 2017;39:293-301 pubmed publisher..In this review, we summarize the mechanisms of PIP trafficking, transcriptional and post-translational regulations, and abiotic stress responses. Moreover, we also discuss the current research trends and future directions on PIPs...