scholarly journals Shot-gun proteome and transcriptome mapping of the jujube floral organ and identification of a pollen-specific S-locus F-box gene

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3588 ◽  
Author(s):  
Ruihong Chen ◽  
Guoliang Chen ◽  
Jian Huang
Keyword(s):  
Protein Profile ◽  
Floral Organ ◽  
Floral Biology ◽  
Reproductive Organ ◽  
S Locus ◽  
Lipid Transfer ◽  
Flowering Season ◽  
New Information ◽  
Liquid Chromatography Tandem Mass ◽  
Systematic Strategy

The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill.) flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In addition, transcriptomics analyses were performed on HiSeq2000 sequencers. In total, 7,853 proteins were identified accounting for nearly 30% of the ‘Junzao’ gene models (27,443). Genes identified in proteome generally showed higher RPKM (reads per kilobase per million mapped reads) values than undetected genes. Gene ontology categories showed that ribosomes and intracellular organelles were the most dominant classes and accounted for 17.0% and 14.0% of the proteome mass, respectively. The top-ranking proteins with iBAQ >1010 included non-specific lipid transfer proteins, histones, actin-related proteins, fructose-bisphosphate aldolase, Bet v I type allergens, etc. In addition, we identified one pollen-specificity S-locus F-box-like gene located on the same chromosome as the S-RNase gene. Both of these may activate the behaviour of gametophyte self-incompatibility in jujube. These results reflected the protein profile features of jujube flowers and contributes new information important to the jujube breeding system.

scholarly journals Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Lulu Wang ◽  
Yi Li ◽  
Xingyue Jin ◽  
Liping Liu ◽  
Xiaozhuan Dai ◽  
...  
Keyword(s):  
Fruit Development ◽  
Gene Networks ◽  
Floral Organ ◽  
Reproductive Organ ◽  
Molecular Networks ◽  
Organ Growth ◽  
Petal Development ◽  
Genomic Resource

AbstractProper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth.

scholarly journals Determination of floral development stages in ‘Cabernet Sauvignon’ (Vitis vinifera L. cv.): highlighting the manifestation of stamens and pistil primordia with new intermediate stages linking the phenological stages

2019 ◽  
Vol 34 (2) ◽  
pp. 84-90
Author(s):  
Z. Gökbayrak ◽  
H. Engin
Keyword(s):  
Fold Increase ◽  
Floral Organ ◽  
Reproductive Organ ◽  
Vitis Vinifera L ◽  
Initial Growth ◽  
Phenological Stages ◽  
Flower Primordia ◽  
Pistil Length ◽  
The Individual ◽  
Intensive Work

Despite relatively intensive work on the development of inflorescence primordia during grapevine growth in season one, some informational gaps are present in the flower and floral organ development in the season two. In addition, concurrents events of phenology and formation of flowers and floral parts has not been dealt with. With the aid of digital imaging, this research had three objectives; a) describe the developmental events that take place during and after bud break in the buds and in the individual flowers in terms of differentiation, b) match these events with phenological stages, and c) determine size-related growth of the floral organs. After careful dissecting and examination of the samples under microscopy, taken ever 5-10 days between March 20 and May 10 in 2016, the results indicated that highly esteemed works regarding the reproductive anatomy of grapevines needed some additional stages to fully describe events in the stamen and pistil primordia after the appearance of petal primordia. Five intermediate stages were added to the stages of “formation of flowers”. Differentiation of inflorescence and individual flowers occurred in the second season as the buds swelled in the spring. Stamens and pistil could be seen about 3 weeks later and completed their initial growth in another 3 weeks. Flower primordia was visible on April 1 and showed a more than 9-fold increase over the course of 5 to 6 weeks. flowers increased their width and their length more than 9- and 15-fold, respectively, between stage 8.1 (April 1) and 10.3 (May 10). At first, they were wider than they were longer, but at later stages they grew longitudinally. Reproductive organ primordia were visualized around the time of 2-4 leaves separated on the shoots. Signs of generative parts become apparent in late April. Anthers were the smallest in the flower. Filaments, on the other hand, elongated almost 7-fold in a period of 20 days. Gynoecium growth was the most impressive and total pistil length increased from 52.8 to 162 μm, ovary width from 40.4 to 99.8 μm, and stigma diameter from 9.96 to 44.9 μm in twenty days. By the time the pistil took its final shape, 6-8 leaves grew on the shoot during which inflorescence could also be seen.

HUA ENHANCER2, a putative DExH-box RNA helicase, maintains homeotic B and C gene expression inArabidopsis

Development ◽  
2002 ◽  
Vol 129 (7) ◽  
pp. 1569-1581 ◽  
Author(s):  
Tamara L. Western ◽  
Yulan Cheng ◽  
Jun Liu ◽  
Xuemei Chen
Keyword(s):  
Gene Expression ◽  
Floral Organ ◽  
Rna Helicase ◽  
Reproductive Organ ◽  
Recessive Mutation ◽  
Homeotic Genes ◽  
Organ Identity ◽  
Quadruple Mutant ◽  
Normal Spacing ◽  
Floral Homeotic

Reproductive organ identity in Arabidopsis is controlled by the B, C and SEPALLATA classes of floral homeotic genes. We have identified a recessive mutation in a novel gene, HUA ENHANCER2, which, when combined with mutations in two weak class C genes, HUA1 and HUA2, leads to the production of third whorl sepal-petal-stamens and fourth whorl sepal-carpels. Quadruple mutant analysis and in situ localization of A, B, C and SEPALLATA floral homeotic RNAs suggest that HUA ENHANCER2 is required for the maintenance of B and C gene expression in the reproductive whorls. In addition to its role in floral homeotic gene expression, HUA ENHANCER2 is required for normal spacing and number of perianth organ primordia. We show that HUA ENHANCER2 encodes a putative DExH-box RNA helicase that is expressed in specific patterns in the inflorescence meristem and developing flowers. As a possible ortholog of the yeast exosome-associated protein, Dob1p (Mtr4p), HUA ENHANCER2 may affect floral organ spacing and identity through the regulation of protein synthesis or mRNA degradation. Therefore, our studies on HUA ENHANCER2 not only demonstrate that B and C gene expression is established and maintained separately, but also implicate the existence of post-transcriptional mechanisms in the maintenance of B and C gene expression.

3D Mapping Reveals a Complex and Transient Interstitial Matrix During Murine Kidney Development

2021 ◽  
pp. ASN.2020081204
Author(s):  
Sarah N. Lipp ◽  
Kathryn R. Jacobson ◽  
David S. Hains ◽  
Andrew L. Schwarderer ◽  
Sarah Calve
Keyword(s):  
Basement Membrane ◽  
Kidney Development ◽  
3D Visualization ◽  
3D Structure ◽  
Matrix Proteins ◽  
Protein Abundance ◽  
New Information ◽  
Liquid Chromatography Tandem Mass ◽  
Transient Elevation

BackgroundThe extracellular matrix (ECM) is a network of proteins and glycosaminoglycans that provides structural and biochemical cues to cells. In the kidney, the ECM is critical for nephrogenesis; however, the dynamics of ECM composition and how it relates to 3D structure during development is unknown.MethodsUsing embryonic day 14.5 (E14.5), E18.5, postnatal day 3 (P3), and adult kidneys, we fractionated proteins based on differential solubilities, performed liquid chromatography–tandem mass spectrometry, and identified changes in ECM protein content (matrisome). Decellularized kidneys were stained for ECM proteins and imaged in 3D using confocal microscopy.ResultsWe observed an increase in interstitial ECM that connects the stromal mesenchyme to the basement membrane (TNXB, COL6A1, COL6A2, COL6A3) between the embryo and adult, and a transient elevation of interstitial matrix proteins (COL5A2, COL12A1, COL26A1, ELN, EMID1, FBN1, LTBP4, THSD4) at perinatal time points. Basement membrane proteins critical for metanephric induction (FRAS1, FREM2) were highest in abundance in the embryo, whereas proteins necessary for integrity of the glomerular basement membrane (COL4A3, COL4A4, COL4A5, LAMB2) were more abundant in the adult. 3D visualization revealed a complex interstitial matrix that dramatically changed over development, including the perinatal formation of fibrillar structures that appear to support the medullary rays.ConclusionBy correlating 3D ECM spatiotemporal organization with global protein abundance, we revealed novel changes in the interstitial matrix during kidney development. This new information regarding the ECM in developing kidneys offers the potential to inform the design of regenerative scaffolds that can guide nephrogenesis in vitro.

scholarly journals Proteome of the Triatomine Digestive Tract: From Catalytic to Immune Pathways; Focusing on Annexin Expression

2020 ◽  
Vol 7 ◽  
Author(s):  
Marcia Gumiel ◽  
Debora Passos de Mattos ◽  
Cecília Stahl Vieira ◽  
Caroline Silva Moraes ◽  
Carlos José de Carvalho Moreira ◽  
...  
Keyword(s):  
Immune System ◽  
Digestive Tract ◽  
Protein Profile ◽  
Humoral Response ◽  
Triatoma Infestans ◽  
Intestinal Epithelial ◽  
Liquid Chromatography Tandem Mass ◽  
And Function ◽  
Phylogenetic Affinities ◽  
Insect Innate Immunity

Rhodnius prolixus, Panstrongylus megistus, Triatoma infestans, and Dipetalogaster maxima are all triatomines and potential vectors of the protozoan Trypanosoma cruzi responsible for human Chagas’ disease. Considering that the T. cruzi’s cycle occurs inside the triatomine digestive tract (TDT), the analysis of the TDT protein profile is an essential step to understand TDT physiology during T. cruzi infection. To characterize the protein profile of TDT of D. maxima, P. megistus, R. prolixus, and T. infestans, a shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was applied in this report. Most proteins were found to be closely related to metabolic pathways such as gluconeogenesis/glycolysis, citrate cycle, fatty acid metabolism, oxidative phosphorylation, but also to the immune system. We annotated this new proteome contribution gathering it with those previously published in accordance with Gene Ontology and KEGG. Enzymes were classified in terms of class, acceptor, and function, while the proteins from the immune system were annotated by reference to the pathways of humoral response, cell cycle regulation, Toll, IMD, JNK, Jak-STAT, and MAPK, as available from the Insect Innate Immunity Database (IIID). These pathways were further subclassified in recognition, signaling, response, coagulation, melanization and none. Finally, phylogenetic affinities and gene expression of annexins were investigated for understanding their role in the protection and homeostasis of intestinal epithelial cells against the inflammation.

scholarly journals Floral structure and genetical differences of sandalwood variants in Gunung Sewu (Java, Indonesia), and its effects on breeding systems and reproductive ability

2019 ◽  
Vol 20 (2) ◽  
pp. 393-404
Author(s):  
YENI W.N. RATNANINGRUM ◽  
AFFAN KURNIAWAN
Keyword(s):  
Genetic Diversity ◽  
Seed Viability ◽  
Floral Organ ◽  
Rehabilitation Program ◽  
Breeding Systems ◽  
Floral Structure ◽  
Isoenzyme Analysis ◽  
Reproductive Ability ◽  
Flowering Season ◽  
Small Flower

Ratnaningrum YWN, Kurniawan A. 2019. Floral structure and genetical differences of sandalwood variants in Gunung Sewu (Java, Indonesia), and its effects on breeding systems and reproductive ability. Biodiversitas 20: 393-404. Our preliminary studies reported that the failure on rehabilitation program of sandalwood, an endangered endemic species in Indonesia, was caused by low viability and survival due to reproductive failure. New sandalwood landraces in Gunung Sewu Geopark, Java island consist of three variants (YBF, refers to "yellow big flower"; RBF, "red big flower"; and RSF, "red small flower") differed by floral structures. This study was made on three sandalwood variants grew in four landraces representing landscape zones in Gunung Sewu, from April to September 2017 flowering season. This advanced study was aimed to estimate the differences in floral structures and genetic diversity among variants, and their effects on breeding systems and reproductive ability. Floral organ measurements were made on each variant. Isoenzyme analysis was conducted to estimate the genetic diversity of each variant and in each site. Mating systems were estimated by Index of Incompatibility (ISI) and Cruden's Out Crossing Index (OCI) methods. Reproductive ability was measured by counting Pollination Effectiveness, Reproductive Success and seed viability. Results found that six loci were polymorphic in most of sites and variants, with exception for Petir and Bejiharjo sites and YBF variant. Observed heterozygosity varied with sites but was similar among variants. Some of diversity existed among both sites and variants. The OCI value scored more than 3 for all variants, indicating an outbreeding mating system. RSF showed higher OCI value compared to both RBF and YBF. Bleberan and Nglanggeran, the outcrossed and completely self-incompatible populations (ISI = 0), failed to produce selfed seeds. In such highly outcrossing, self-incompatible populations, the highest seed set was gained from intraspecific-crossed pollination. Contrastly, the inbreeding and self-compatible populations (ISI = 3 to ∞), Petir and Bejiharjo, tended to alter its matting system to be more inbreeding. Reproductive ability differed by sites but was similar among variants.

scholarly journals Method of extraction and proteome profiling of mycobacteria using liquid chromatography-high resolution mass spectrometry

2020 ◽  
Vol 2 (11) ◽  
Author(s):  
Amol Bajaj ◽  
Suraj Saraswat ◽  
Joanna Freeke ◽  
Adam Barker
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Protein Identification ◽  
High Resolution Mass Spectrometry ◽  
Massively Parallel Sequencing ◽  
Protein Profile ◽  
Cell Lysis ◽  
Mycolic Acid ◽  
Extraction Solvent ◽  
Liquid Chromatography Tandem Mass

AbstractAdvances in massively parallel sequencing, of complete bacterial genomes, have led to many novel findings in the field of genomics. However, these data often lack correlation with expressed protein profiles. It has been demonstrated that even very closely related genomes, such as in mycobacteria, express drastically different phenotypes. These phenotypes often have major roles in pathogenicity. Therefore, it is just as important to have a method for examining the proteome of a bacterium as well as its genome. These studies are further complicated in mycobacteria due to the cell wall and mycolic acid. A comprehensive method for the identification and characterization of the whole mycobacterium protein profile is needed. In the present study, a simple, sensitive, and specific liquid chromatography tandem mass spectrometry method was developed for the extraction, purification and profiling the mycobacterial proteome in various species. During development, sonication and bead-beating cell lysis protocol was tested using 15% Acetonitrile and 6 M guanidine-HCl (GuHCl) as extraction solvent. Sonication lysis in 6 M GuHCl with glass beads was the preferred method for cell lysis. This method was developed using reverse phase liquid chromatography and a Q Exactive ™ Plus Orbitrap™ mass spectrometer for peptide and protein identification. Bottom-up liquid chromatography-mass spectrometry LC–MS analysis resulted in identification of greater than 2500 proteins.

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