The Landscape of Autophagy-Related (ATG) Genes and Functional Characterization of TaVAMP727 to Autophagy in Wheat

Autophagy is an indispensable biological process and plays crucial roles in plant growth and plant responses to both biotic and abiotic stresses. This study systematically identified autophagy-related proteins (ATGs) in wheat and its diploid and tetraploid progenitors and investigated their genomic organization, structure characteristics, expression patterns, genetic variation, and regulation network. We identified a total of 77, 51, 29, and 30 ATGs in wheat, wild emmer, T. urartu and A. tauschii, respectively, and grouped them into 19 subfamilies. We found that these autophagy-related genes (ATGs) suffered various degrees of selection during the wheat’s domestication and breeding processes. The genetic variations in the promoter region of Ta2A_ATG8a were associated with differences in seed size, which might be artificially selected for during the domestication process of tetraploid wheat. Overexpression of TaVAMP727 improved the cold, drought, and salt stresses resistance of the transgenic Arabidopsis and wheat. It also promoted wheat heading by regulating the expression of most ATGs. Our findings demonstrate how ATGs regulate wheat plant development and improve abiotic stress resistance. The results presented here provide the basis for wheat breeding programs for selecting varieties of higher yield which are capable of growing in colder, drier, and saltier areas.

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Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽

10.3390/agronomy11071312 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1312

Author(s):

Jia Liu ◽

Weicong Qi ◽

Haiying Lu ◽

Hongbo Shao ◽

Dayong Zhang

Keyword(s):

Plasma Membrane ◽

Salt Stress ◽

Salt Tolerance ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Early Gene ◽

Plant Responses ◽

Constitutive Overexpression ◽

Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

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Identification and Functional Characterization of a Cold-Related Protein, BcHHP5, in Pak-Choi (Brassica rapa ssp. chinensis)

International Journal of Molecular Sciences ◽

10.3390/ijms20010093 ◽

2018 ◽

Vol 20 (1) ◽

pp. 93

Author(s):

Jin Wang ◽

Feiyi Huang ◽

Xiong You ◽

Xilin Hou

Keyword(s):

Brassica Rapa ◽

Abiotic Stresses ◽

Quantitative Polymerase Chain Reaction ◽

Functional Characterization ◽

Regulation Mechanism ◽

Pak Choi ◽

Negative Effect ◽

Polymerase Chain ◽

Related Proteins

In plants, heptahelical proteins (HHPs) have been shown to respond to a variety of abiotic stresses, including cold stress. Up to the present, the regulation mechanism of HHP5 under low temperature stress remains unclear. In this study, BcHHP5 was isolated from Pak-choi (Brassica rapa ssp. chinensis cv. Suzhouqing). Sequence analysis and phylogenetic analysis indicated that BcHHP5 in Pak-choi is similar to AtHHP5 in Arabidopsis thaliana. Structure analysis showed that the structure of the BcHHP5 protein is relatively stable and highly conservative. Subcellular localization indicated that BcHHP5 was localized on the cell membrane and nuclear membrane. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcHHP5 was induced to express by cold and other abiotic stresses. In Pak-choi, BcHHP5-silenced assay, inhibiting the action of endogenous BcHHP5, indicated that BcHHP5-silenced might have a negative effect on cold tolerance, which was further confirmed. All of these results indicate that BcHHP5 might play a role in abiotic response. This work can serve as a reference for the functional analysis of other cold-related proteins from Pak-choi in the future.

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Expression of Glucose Metabolism-Related Proteins in Adrenal Neoplasms

Pathobiology ◽

10.1159/000518208 ◽

2021 ◽

pp. 1-10

Author(s):

Eun Kyung Kim ◽

Hye Min Kim ◽

Ja Seung Koo

Keyword(s):

Prognostic Factors ◽

Glucose Metabolism ◽

Expression Patterns ◽

Univariate Analysis ◽

Hexokinase Ii ◽

Expression Levels ◽

Adrenal Cortical Adenoma ◽

Adrenal Neoplasms ◽

Cox Analysis ◽

Related Proteins

Purpose: The aim of this study was to investigate the expression patterns of glucose metabolism-related proteins and their clinicopathologic implications in adrenal cortical neoplasms (ACN) and pheochromocytoma (PCC). Methods: Immunohistochemical staining was performed to evaluate glucose metabolism-related proteins (GLUT1, CAIX, hexokinase II, G6PDH, PHGDH, and SHMT1) in 132 ACN cases (115 adrenal cortical adenoma [ACA] and 17 adrenal cortical carcinoma [ACC]) and 189 PCC cases. Results: Expression levels of GLUT1 in tumor cells ([T]; p < 0.001), GLUT1 in stromal cells ([S]; p < 0.001), G6PDH (p < 0.001), and SHMT1 (p = 0.002) were higher in ACN than in PCC. GLUT1 (T; p = 0.045) and PHGDH (p = 0.043) levels were higher in ACC than in ACA. In a univariate analysis of ACN, GLUT1 (T; p = 0.017), CAIX (S; p = 0.003), and PHGDH (p = 0.009) levels were correlated with a shorter overall survival (OS). GLUT1 (T; p = 0.001) and PHGDH (p < 0.001) were related to a shorter OS in PCC. GLUT1 (T) positivity (p = 0.043) in ACN predicted a poor OS in a multivariate Cox analysis. In PCC, high GAPP score (p = 0.026), GLUT1 (T; p = 0.002), and PHGDH (p < 0.001) were independent prognostic factors for poor OS. Conclusions: The adrenal gland tumors ACN and PCC had different expression patterns of glucose metabolism-related proteins (GLUT1, G6PDH, and SHMT1), with higher expression levels in ACN than in PCC. GLUT1 and PHGDH were significant prognostic factors in these adrenal neoplasms.

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Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics

Current Genomics ◽

10.2174/1389202922666211130143328 ◽

2021 ◽

Vol 22 ◽

Author(s):

Soma Ghosh ◽

Malathi Bheri ◽

Girdhar K. Pandey

Keyword(s):

Functional Genomics ◽

Protein Kinases ◽

Regulatory Networks ◽

Crop Improvement ◽

Functional Characterization ◽

Genomic Analysis ◽

Major Elements ◽

Model Systems ◽

Plant Responses ◽

Dependent Protein

: Plant systems have developed calcium (Ca2+) signaling as an important mechanism of regulation of stress perception, developmental cues, and responsive gene expression. The post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery involve Ca2+ sensors and responders such as Calmodulin (CaM), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMK), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be the stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

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Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20225796 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5796

Author(s):

Qianqian Zhou ◽

Qingchang Li ◽

Peng Li ◽

Songtao Zhang ◽

Che Liu ◽

...

Keyword(s):

Gene Family ◽

Physiological Stress ◽

Expression Patterns ◽

Functional Characterization ◽

Hormone Treatment ◽

Nicotiana Sylvestris ◽

Regulatory Elements ◽

Evolutionary Analysis ◽

Comprehensive Overview ◽

Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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Placental PAGs: gene origins, expression patterns, and use as markers of pregnancy

Reproduction ◽

10.1530/rep-14-0485 ◽

2015 ◽

Vol 149 (3) ◽

pp. R115-R126 ◽

Cited By ~ 55

Author(s):

Rhianna M Wallace ◽

Ky G Pohler ◽

Michael F Smith ◽

Jonathan A Green

Keyword(s):

Expression Patterns ◽

Spatial Expression ◽

Putative Role ◽

Pregnancy Status ◽

Temporal And Spatial ◽

Related Proteins ◽

In Pregnancy

Pregnancy-associated glycoproteins (PAGs) are abundantly expressed products of the placenta of species within the Cetartiodactyla order (even-toed ungulates). They are restricted to this order and they are particularly numerous in the Bovidae. The PAGs exhibit a range of temporal and spatial expression patterns by the placental trophoblasts and probably represent a group of related proteins that perform a range of distinct functions in the epitheliochorial and synepitheliochorial placental forms. This review presents an overview of the origins of the PAGs, a summary of PAG expression patterns, and their use as markers of pregnancy status. Speculations about their putative role(s) in pregnancy are also presented.

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NPF genes excavation and their expression response to vernalization and nitrogen deficiency in allotetraploid rapeseed

10.21203/rs.3.rs-236072/v1 ◽

2021 ◽

Author(s):

Hongbo Chao ◽

Jianjie He ◽

Weiguo Zhao ◽

Hong Fu ◽

Yingpeng Hua ◽

...

Keyword(s):

Expression Patterns ◽

Functional Characterization ◽

Nitrogen Deficiency ◽

Enrichment Analysis ◽

Functional Differentiation ◽

Peptide Transporter ◽

Peptide Transporters ◽

Transporter Family ◽

Expression Response ◽

Metabolite Content

Abstract Background The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY (NPF) genes, initially characterized as nitrate or peptide transporters in plants, involve in the transport of a large variety of substrates including amino acids, nitrate, auxin (IAA), jasmonates (JAs), abscisic acid (ABA) and gibberellins (GAs) and glucosinolates. The evolution and expression diversification of genes determine their functional differentiation in polyploid species. Results Among 169 NPF genes excavated in Brassica napus, 97 B. napus NPF (BnaNPF) genes evolved from B. rapa, and 72 BnaNPF genes from B. olereaca. They unevenly distributed on B. napus genome and exhibited obvious synteny with NPF genes in Arabidopsis thaliana, B. rapa and B. olereaca. BnaNPF genes were identified to show diversified expression patterns in 90 different organs or tissues based on transcriptome profile data. Besides, they exhibited complex expression changes in the development process of leaves, silique wall and seeds, which indicated that the expression of BnaNPF genes maybe respond to altered phytohormone and secondary metabolite content through combining with promoter elements enrichment analysis. Furthermore, many BnaNPF genes were detected to response to vernalization with two different patterns and 20 BnaNPF genes responded to nitrate deficiency. Conclusion The evolution of BnaNPF genes and their expression pattern including response to vernalization and nitrogen deficiency were characterized and provide valuable information for further functional characterization in rapeseed.

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Identification of Regulatory circRNAs Involved in the Pathogenesis of Acute Myocardial Infarction

Frontiers in Genetics ◽

10.3389/fgene.2020.626492 ◽

2021 ◽

Vol 11 ◽

Author(s):

Cuimei Zhao ◽

Jingjing Liu ◽

Wen Ge ◽

Zhi Li ◽

Mengwei Lv ◽

...

Keyword(s):

Myocardial Infarction ◽

Acute Myocardial Infarction ◽

Coronary Arteries ◽

Expression Profiles ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Functional Characterization ◽

High Morbidity ◽

The Impact ◽

Runx1 Expression

BackgroundAcute myocardial infarction (AMI) has high morbidity and mortality worldwide. However, the pathogenesis of AMI is still unclear, and the impact of circular RNAs (circRNAs) on AMI has rarely been recognized and needs to be explored.Materials and MethodsThe circRNA array was applied to investigate the expression level of circRNAs in the blood samples of coronary arteries of three AMI patients and three normal persons. Principal component analysis (PCA) and unsupervised clustering analysis were performed to reveal the distinguished expression patterns of circRNAs. The miRNA expression profiles of AMI patients were identified from a public dataset from the Gene Expression Omnibus (GEO) database (GSE31568). The miRNA binding sites on the circRNAs were predicted by miRanda. The miRNA enrichment analysis and annotation tool were used to explore the pathways that the dysregulated circRNAs may participate in.ResultsIn total, 142 differentially expressed circRNAs, including 89 upregulated and 53 downregulated in AMI samples, were identified by the differential expression analysis. AMI patients had quite different circRNA expression profiles to those of normal controls. Functional characterization revealed that circRNAs that had the potential to regulate miRNAs were mainly involved in seven pathways, such as the Runt-related transcription factor-1 (RUNX1) expression and activity-related pathway. Specifically, hsa_circRNA_001654, hsa_circRNA_091761, hsa_circRNA_405624, and hsa_circRNA_406698 were predicted to sponge four miRNAs including hsa-miR-491-3p, hsa-miR-646, hsa-miR-603, and hsa-miR-922, thereby regulating RUNX1 expression or activity.ConclusionWe identified dysregulated blood circRNAs in the coronary arteries of AMI patients and predicted that four upregulated circRNAs were involved in the regulation of RUNX1 expression or activity through sponging four miRNAs.

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