Data Mining Nitrogen-Responsive Gene Expression for Source–Sink Relations and Indicators of N Status in Potato

Potato tuber yields depend on nitrogen (N) supply, which affects source–sink relations. Transcriptome sequencing of the foliar source using a single field trial identified gene expression responsive to 180 kg N ha−1. The expression of N-responsive genes was further analyzed in the next stage using a NanoString nCounter over an expanded number of foliar samples from seven field trials with varying N rates, sites, and cultivars. Least absolute shrinkage and selection operator (LASSO) regression models of gene expression predictive of yield, total plant N uptake, and tuber-specific gravity (proxy for dry matter) were built. Genes in the LASSO model for yield were associated with source–sink partitioning. A key gene regulating tuberization and senescence, StSP6A Flowering locus T, was found in the LASSO model predicting tuber yield, but not the other models. An aminotransferase involved in photorespiratory N assimilation and amino acid biosynthesis was found in all LASSO models. Other genes functioning in amino acid biosynthesis and integration of sulfur (S) and N metabolism were also found in the yield prediction model. The study provides insights on N responses in foliage of potato plants that affect source–sink partitioning. Additionally, N-responsive genes predictive of yield are candidate indicators of N status.

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Highly expressed amino acid biosynthesis genes revealed by global gene expression analysis of Salmonella enterica serovar Enteritidis during growth in whole egg are not essential for this growth

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2016.02.015 ◽

2016 ◽

Vol 224 ◽

pp. 40-46 ◽

Cited By ~ 8

Author(s):

Džiuginta Jakočiūnė ◽

Ana Herrero-Fresno ◽

Lotte Jelsbak ◽

John Elmerdahl Olsen

Keyword(s):

Gene Expression ◽

Amino Acid ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Global Gene Expression ◽

Amino Acid Biosynthesis ◽

Acid Biosynthesis ◽

Salmonella Enterica Serovar Enteritidis ◽

Global Gene Expression Analysis ◽

Whole Egg

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Transcriptional and Translational Regulation of Gene Expression in the General Control of Amino-Acid Biosynthesis in Saccharomyces cerevisiae

Progress in Nucleic Acid Research and Molecular Biology ◽

10.1016/s0079-6603(08)60712-6 ◽

1990 ◽

pp. 195-240 ◽

Cited By ~ 33

Author(s):

Alan G. Hinnebusch

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Amino Acid ◽

Translational Regulation ◽

Regulation Of Gene Expression ◽

Amino Acid Biosynthesis ◽

General Control ◽

Acid Biosynthesis ◽

Transcriptional And Translational Regulation

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Integration of the metabolome and transcriptome reveals the mechanism of resistance to low nitrogen supply in wild bermudagrass (Cynodon dactylon (L.) Pers.) roots

BMC Plant Biology ◽

10.1186/s12870-021-03259-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dandan Li ◽

Jianxiu Liu ◽

Junqin Zong ◽

Hailin Guo ◽

Jianjian Li ◽

...

Keyword(s):

Protein Synthesis ◽

Amino Acid ◽

Cynodon Dactylon ◽

Amino Acid Content ◽

Trna Synthetase ◽

Amino Acid Biosynthesis ◽

Synthesis Process ◽

Acid Biosynthesis ◽

Natural Habitats ◽

N Assimilation

Abstract Background Nitrogen (N) is an essential macronutrient that significantly affects turf quality. Commercial cultivars of bermudagrass (Cynodon dactylon (L.) Pers.) require large amounts of nitrogenous fertilizer. Wild bermudagrass germplasm from natural habitats with poor nutrition and diverse N distributions is an important source for low-N-tolerant cultivated bermudagrass breeding. However, the mechanisms underlying the differences in N utilization among wild germplasm resources of bermudagrass are not clear. Results To clarify the low N tolerance mechanism in wild bermudagrass germplasm, the growth, physiology, metabolome and transcriptome of two wild accessions, C291 (low-N-tolerant) and C716 (low-N-sensitive), were investigated. The results showed that root growth was less inhibited in low-N-tolerant C291 than in low-N-sensitive C716 under low N conditions; the root dry weight, soluble protein content and free amino acid content of C291 did not differ from those of the control, while those of C716 were significantly decreased. Down-regulation of N acquisition, primary N assimilation and amino acid biosynthesis was less pronounced in C291 than in C716 under low N conditions; glycolysis and the tricarboxylic acid (TCA) cycle pathway were also down-regulated, accompanied by a decrease in the biosynthesis of amino acids; strikingly, processes such as translation, biosynthesis of the structural constituent of ribosome, and the expression of individual aminoacyl-tRNA synthetase genes, most of genes associated with ribosomes related to protein synthesis were all up-regulated in C291, but down-regulated in C716. Conclusions Overall, low-N-tolerant wild bermudagrass tolerated low N nutrition by reducing N primary assimilation and amino acid biosynthesis, while promoting the root protein synthesis process and thereby maintaining root N status and normal growth.

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Candida albicans Biofilms: a Developmental State Associated With Specific and Stable Gene Expression Patterns

Eukaryotic Cell ◽

10.1128/ec.3.2.536-545.2004 ◽

2004 ◽

Vol 3 (2) ◽

pp. 536-545 ◽

Cited By ~ 243

Author(s):

Susana García-Sánchez ◽

Sylvie Aubert ◽

Ismaïl Iraqui ◽

Guilhem Janbon ◽

Jean-Marc Ghigo ◽

...

Keyword(s):

Gene Expression ◽

Candida Albicans ◽

Amino Acid ◽

Expression Patterns ◽

Developmental State ◽

Amino Acid Biosynthesis ◽

Antifungal Drugs ◽

Stable Gene ◽

Acid Biosynthesis ◽

Mycelial Development

ABSTRACT Like many bacteria, yeast species can form biofilms on several surfaces. Candida albicans colonizes the surfaces of catheters, prostheses, and epithelia, forming biofilms that are extremely resistant to antifungal drugs. We have used transcript profiling to investigate the specific properties of C. albicans biofilms. Biofilm and planktonic cultures produced under different conditions of nutrient flow, aerobiosis, or glucose concentration were compared by overall gene expression correlation. Correlation was much higher between biofilms than planktonic populations irrespective of the growth conditions, indicating that biofilm populations formed in different environments display very similar and specific transcript profiles. A first cluster of 325 differentially expressed genes was identified. In agreement with the overrepresentation of amino acid biosynthesis genes in this cluster, Gcn4p, a regulator of amino acid metabolism, was shown to be required for normal biofilm growth. To identify biofilm-related genes that are independent of mycelial development, we studied the transcriptome of biofilms produced by a wild-type, hypha-producing strain and a cph1/cph1 efg1/efg1 strain defective for hypha production. This analysis identified a cluster of 317 genes expressed independently of hypha formation, whereas 86 genes were dependent on mycelial development. Both sets revealed the activation of the sulfur-amino acid biosynthesis pathway as a feature of C. albicans biofilms.

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