scholarly journals Proteomics

2021 ◽  
Vol 11 (12) ◽  
pp. 158-189
Author(s):  
S. Dolomatov ◽  
V. Kazakova ◽  
W. Zukow
Keyword(s):  
Semantic Content ◽  
Covalent Modification ◽  
Original Structure ◽  
Amino Acid Residues ◽  
Adaptive Responses ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Cell Tissue ◽  
Processing Pathways ◽  
Protein Functions

Proteomics is a branch of molecular biology that deals with the identification and quantification of proteins in living objects, as well as the analysis of protein functions and their interactions. Proteomics is studied by proteins that are expressed in a given cell, tissue or organism over a period of time (under certain conditions). It is known that information about the primary structure of a protein (the sequence of amino acid residues in a protein) is contained in a structural gene in the form of a codon sequence (genetic code). On the other hand, less than 10% of genes are functionally active (expressed) in the somatic cells of our body. Moreover, a distinct tissue-specific expression of genes is observed. This, in turn, leads to the peculiarities of the qualitative composition of the synthesized proteins in various tissues. No less important is the fact that the total amount of proteins synthesized by our tissues is much greater than the total number of structural genes containing information about their original structure. This phenomenon is explained by the activity of such mechanisms as alternative splicing and a wide variety of post-translational peptide processing pathways (covalent modification of a polypeptide synthesized on the ribosome) in health and disease. Thus, even a brief review of the semantic content of the term "proteomics" indicates an extremely complex system of protein molecules in our body, which plays a fundamental role in maintaining homeostasis and is involved in the formation of adaptive responses in response to adverse changes in the internal and external environment.

Cell-, tissue-, sex- and developmental stage-specific expression of mouse flavin-containing monooxygenases (Fmos)

2004 ◽  
Vol 68 (1) ◽  
pp. 73-83 ◽  
Author(s):  
Azara Janmohamed ◽  
Diana Hernandez ◽  
Ian R Phillips ◽  
Elizabeth A Shephard
Keyword(s):  
Developmental Stage ◽  
Specific Expression ◽  
Cell Tissue

scholarly journals Molecular and physiological characterization of the effects of auxin-enriched rootstock on grafting

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Longmei Zhai ◽  
Xiaomin Wang ◽  
Dan Tang ◽  
Qi Qi ◽  
Huseyin Yer ◽  
...  
Keyword(s):  
Callus Formation ◽  
Ethylene Biosynthesis ◽  
Union Formation ◽  
Biosynthetic Gene ◽  
Graft Union ◽  
Specific Expression ◽  
Physiological Characterization ◽  
Graft Healing ◽  
Expression Of Genes ◽  
Or Gene

AbstractsGrafting is a highly useful technique, and its success largely depends on graft union formation. In this study, we found that root-specific expression of the auxin biosynthetic gene iaaM in tobacco, when used as rootstock, resulted in more rapid callus formation and faster graft healing. However, overexpression of the auxin-inactivating iaaL gene in rootstocks delayed graft healing. We observed increased endogenous auxin levels and auxin-responsive DR5::GUS expression in scions of WT/iaaM grafts compared with those found in WT/WT grafts, which suggested that auxin is transported upward from rootstock to scion tissues. A transcriptome analysis showed that auxin enhanced graft union formation through increases in the expression of genes involved in graft healing in both rootstock and scion tissues. We also observed that the ethylene biosynthetic gene ACS1 and the ethylene-responsive gene ERF5 were upregulated in both scions and rootstocks of the WT/iaaM grafts. Furthermore, exogenous applications of the ethylene precursor ACC to the junction of WT/WT grafts promoted graft union formation, whereas application of the ethylene biosynthesis inhibitor AVG delayed graft healing in WT/WT grafts, and the observed delay was less pronounced in the WT/iaaM grafts. These results demonstrated that elevated auxin levels in the iaaM rootstock in combination with the increased auxin levels in scions caused by upward transport/diffusion enhanced graft union formation and that ethylene was partially responsible for the effects of auxin on grafting. Our findings showed that grafting success can be enhanced by increasing the auxin levels in rootstocks using transgenic or gene-editing techniques.

scholarly journals Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Chenxu Ye ◽  
Humaira Rasheed ◽  
Yuehua Ran ◽  
Xiaojuan Yang ◽  
Lianxi Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Mapk Pathway ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Genetic Mechanisms ◽  
Ecological Success ◽  
Reproductive Plasticity

Abstract Background The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the isolated workers of Reticulitermes labralis developed into reproductives, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers. Results We identified 38,070 differentially expressed genes and found a pattern of gene expression involved in the differentiation of the workers into reproductives. 12, 543 genes were specifically upregulated in the isolated workers. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into reproductives. Ras functions as a signalling switch regulates the reproductive plasticity of workers. The catalase gene which is related to longevity was up-regulated in reproductives. Conclusion We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into reproductives and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.

Oxygen sensing and molecular adaptation to hypoxia

1996 ◽  
Vol 76 (3) ◽  
pp. 839-885 ◽  
Author(s):  
H. F. Bunn ◽  
R. O. Poyton
Keyword(s):  
Transcription Factors ◽  
Mammalian Cells ◽  
Critical Role ◽  
Hypoxia Inducible Factor ◽  
Signal Transduction Pathway ◽  
Adaptation To Hypoxia ◽  
Adaptive Responses ◽  
Expression Of Genes ◽  
Activation Of Transcription ◽  
Activation Of Oxygen

This review focuses on the molecular stratagems utilized by bacteria, yeast, and mammals in their adaptation to hypoxia. Among this broad range of organisms, changes in oxygen tension appear to be sensed by heme proteins, with subsequent transfer of electrons along a signal transduction pathway which may depend on reactive oxygen species. These heme-based sensors are generally two-domain proteins. Some are hemokinases, while others are flavohemoproteins [flavohemoglobins and NAD(P)H oxidases]. Hypoxia-dependent kinase activation of transcription factors in nitrogen-fixing bacteria bears a striking analogy to the phosphorylation of hypoxia inducible factor-1 (HIF-1) in mammalian cells. Moreover, redox chemistry appears to play a critical role both in the trans-activation of oxygen-responsive genes in unicellular organisms as well as in the activation of HIF-1. In yeast and bacteria, regulatory operons coordinate expression of genes responsible for adaptive responses to hypoxia and hyperoxia. Similarly, in mammals, combinatorial interactions of HIF-1 with other identified transcription factors are required for the hypoxic induction of physiologically important genes.

History of Herbicide-Tolerant Crops, Methods of Development and Current State of the Art – Emphasis on Glyphosate Tolerance

1992 ◽  
Vol 6 (3) ◽  
pp. 626-634 ◽  
Author(s):  
Ganesh M. Kishore ◽  
Stephen R. Padgette ◽  
Robert T. Fraley
Keyword(s):  
Weed Management ◽  
Effective Means ◽  
Shikimate Pathway ◽  
Management Program ◽  
Crop Plants ◽  
Epsp Synthase ◽  
Glyphosate Tolerance ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Wide Range

Weed management is an integral part of agriculture; weeds lower both productivity and quality of agricultural products. A combination of mechanical, chemical, biological, and cultural methods is expected to deliver a sustainable weed management program for the next two decades. While chemical methods offer the most cost effective means of weed management, crop selectivity has hampered the use of the best chemicals for weed management. Recent progress in gene technology has facilitated the introduction and expression of genes to confer a wide range of traits to crop plants. Application of this technology has resulted in the development of crop plant genotypes that are resistant to a specific herbicide. This article describes the progress that has been made by our group toward the introduction of glyphosate tolerance to crop plants. Glyphosate [N-(phosphonomethyl)glycine] kills plants due to inhibition of the biosynthesis of aromatic compounds via the shikimate pathway. Our approach for introduction of glyphosate tolerance is based on insertion and expression in plants of a gene encoding a glyphosate-tolerant 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, a key enzyme of the shikimate pathway. The wild type enzyme present in plants is susceptible to inhibition glyphosate; variants of EPSP synthase have been produced that are less susceptible to inhibition by glyphosate. Expression of genes encoding these variants has been shown to confer glyphosate tolerance to plants. The degree of glyphosate tolerance is related to the tolerance characteristics of the EPSP synthase variant, its substrate activity, targeting to the plastid, and the level of expression of the variant gene. The tissue specificity of expression of the variant EPSP synthase has also been shown to be critical since glyphosate is a systemic herbicide and is translocated to many growing points within the plant. Our studies on glyphosate tolerance have substantially enhanced our understanding of the mode-of-action of glyphosate, the shikimate pathway, and protein sorting within plant cells, as well as developmental and tissue specific expression of genes in plants. Commercial use of glyphosate tolerance technology is expected to affect positively, the weed management arsenal available to the farmers, the sustainability of farm land and groundwater, and promote the use of a “soft” herbicide.

scholarly journals Gene Expression Profiling Indicated Diverse Functions and Characteristics of Core Genes in Pea Aphid

Insects ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 186
Author(s):  
Ruizheng Tian ◽  
Yixiao Huang ◽  
Balachandar Balakrishnan ◽  
Maohua Chen
Keyword(s):  
Expression Profiling ◽  
Insect Pest ◽  
Transcriptome Profiling ◽  
Pea Aphid ◽  
Biological Processes ◽  
Specific Expression ◽  
The Core ◽  
Expression Of Genes ◽  
Pea Aphids ◽  
Core Genes

The pea aphid is a global insect pest, and variable phenotypes can be produced by pea aphids in the same genotype in response to changes in external environmental factors. However, detailed dynamic gene regulation networks and the core markers involved in different biological processes of pea aphids have not yet been reported. In this study, we obtained the published genomic and transcriptomic data, and performed transcriptome profiling of five pea aphid morphs (winged asexual female, wingless asexual female, wingless sexual female, winged male and wingless male) from each of three pea aphid genotypes, i.e., the transcriptomes from a total of 15 types of pea aphids were analyzed and the type-specific expression of genes in five different morphs was identified. The expression profiling was verified by quantitative real-time PCR (qPCR) analysis. Moreover, we determined the expression features and co-expression networks of highly variable genes. We also used the ARACNe method to obtain 263 core genes related to different biological pathways. Additionally, eight of the identified genes were aligned with transcription factor families, indicating that they act as transcription factors and regulate downstream genes. Furthermore, we found reliable markers using random forest methodology to distinguish different morphs of pea aphids. Our study provides a systematic and comprehensive approach for analyzing the core genes that may play important roles in a multitude of biological processes from the insect transcriptomes.

scholarly journals Molecular basis of resistance to organophosphate insecticides in the New World screw-worm fly

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Sophie Tandonnet ◽  
Gisele Antoniazzi Cardoso ◽  
Pedro Mariano-Martins ◽  
Raquel Dietsche Monfardini ◽  
Vanessa A. S. Cunha ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Molecular Basis ◽  
Pyrethroid Resistance ◽  
Management Strategies ◽  
Evolutionary Process ◽  
Specific Expression ◽  
Altered Expression ◽  
Functional Studies ◽  
Expression Of Genes ◽  
Starting Point

Abstract Background The emergence of insecticide resistance is a fast-paced example of the evolutionary process of natural selection. In this study, we investigated the molecular basis of resistance in the myiasis-causing fly Cochliomyia hominivorax (Diptera: Calliphoridae) to dimethyl-organophosphate (OP) insecticides. Methods By sequencing the RNA from surviving larvae treated with dimethyl-OP (resistant condition) and non-treated larvae (control condition), we identified genes displaying condition-specific polymorphisms, as well as those differentially expressed. Results Both analyses revealed that resistant individuals have altered expression and allele-specific expression of genes involved in proteolysis (specifically serine-endopeptidase), olfactory perception and cuticle metabolism, among others. We also confirmed that resistant individuals carry almost invariably the Trp251Ser mutation in the esterase E3, known to confer OP and Pyrethroid resistance. Interestingly, genes involved in metabolic and detoxifying processes (notably cytochrome P450s) were found under-expressed in resistant individuals. An exception to this were esterases, which were found up-regulated. Conclusions These observations suggest that reduced penetration and aversion to dimethyl-OP contaminated food may be important complementary strategies of resistant individuals. The specific genes and processes found are an important starting point for future functional studies. Their role in insecticide resistance merits consideration to better the current pest management strategies.

scholarly journals RNA-seq analysis provides insights into cold stress responses of Xanthomonas citri pv. citri

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jin-Xing Liao ◽  
Kai-Huai Li ◽  
Jin-Pei Wang ◽  
Jia-Ru Deng ◽  
Qiong-Guang Liu ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Low Temperature ◽  
Cold Stress ◽  
Stress Responses ◽  
Citrus Canker ◽  
Transcriptional Analysis ◽  
Adaptive Responses ◽  
Xanthomonas Citri ◽  
Type Iv ◽  
Expression Of Genes

Abstract Background Xanthomonas citri pv. citri (Xcc) is a citrus canker causing Gram-negative bacteria. Currently, little is known about the biological and molecular responses of Xcc to low temperatures. Results Results depicted that low temperature significantly reduced growth and increased biofilm formation and unsaturated fatty acid (UFA) ratio in Xcc. At low temperature Xcc formed branching structured motility. Global transcriptome analysis revealed that low temperature modulates multiple signaling networks and essential cellular processes such as carbon, nitrogen and fatty acid metabolism in Xcc. Differential expression of genes associated with type IV pilus system and pathogenesis are important cellular adaptive responses of Xcc to cold stress. Conclusions Study provides clear insights into biological characteristics and genome-wide transcriptional analysis based molecular mechanism of Xcc in response to low temperature.

scholarly journals Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

2020 ◽  
Vol 48 (21) ◽  
pp. 12348-12364
Author(s):  
Debamita Paul ◽  
Hong Mu ◽  
Amirrasoul Tavakoli ◽  
Qing Dai ◽  
Xuejing Chen ◽  
...  
Keyword(s):  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Original Structure ◽  
Structural Studies ◽  
Gating Mechanism ◽  
Solution Studies ◽  
Nucleotide Excision ◽  
Protein Functions ◽  
Dynamics Simulations

Abstract XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells.

Sign in / Sign up

Export Citation Format

Share Document