scholarly journals Genome-Wide Analysis of Major Facilitator Superfamily and Its Expression in Response of Poplar to Fusarium oxysporum

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Diao ◽  
Shuxuan Li ◽  
Ling Ma ◽  
Ping Zhang ◽  
Jianyang Bai ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Populus Trichocarpa ◽  
Major Facilitator Superfamily ◽  
Specific Gene ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Duplication Events ◽  
Gene Structures ◽  
Major Facilitator

The major facilitator superfamily (MFS) is one of the largest known membrane transporter families. MFSs are involved in many essential functions, but studies on the MFS family in poplar have not yet been reported. Here, we identified 41 MFS genes from Populus trichocarpa (PtrMFSs). We built a phylogenetic tree, which clearly divided members of PtrMFS into six groups with specific gene structures and protein motifs/domains. The promoter regions contain various cis-acting elements involved in stress and hormone responsiveness. Genes derived from segmental duplication events are unevenly distributed in 17 poplar chromosomes. Collinearity analysis showed that PtrMFS genes are conserved and homologous to corresponding genes from four other species. Transcriptome data indicated that 40 poplar MFS genes were differentially expressed when treated with Fusarium oxysporum. Co-expression networks and gene function annotations of MFS genes showed that MFS genes tightly co-regulated and closely related in function of transmembrane transport. Taken together, we systematically analyzed structure and function of genes and proteins in the PtrMFS family. Evidence indicated that poplar MFS genes play key roles in plant development and response to a biological stressor.

scholarly journals Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1669
Author(s):  
Angelo De Paolis ◽  
Sofia Caretto ◽  
Angela Quarta ◽  
Gian-Pietro Di Sansebastiano ◽  
Irene Sbrocca ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Antimalarial Activity ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

scholarly journals Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1134
Author(s):  
Shichao Liu ◽  
Ruibin Sun ◽  
Xiaojian Zhang ◽  
Zili Feng ◽  
Feng Wei ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Biotic And Abiotic Stresses ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
Duplication Events ◽  
Polyethylene Glycol 6000 ◽  
Similar Gene

The 12-oxo-phytodienoic acid reductases (OPRs) have been proven to play a major role in plant development and growth. Although the classification and functions of OPRs have been well understood in Arabidopsis, tomato, rice, maize, and wheat, the information of OPR genes in cotton genome and their responses to biotic and abiotic stresses have not been reported. In this study, we found 10 and 9 OPR genes in Gossypium hirsutum and Gossypium barbadense, respectively. They were classified into three groups, based on the similar gene structure and conserved protein motifs. These OPR genes just located on chromosome 01, chromosome 05, and chromosome 06. In addition, the whole genome duplication (WGD) or segmental duplication events contributed to the evolution of the OPR gene family. The analyses of cis-acting regulatory elements of GhOPRs showed that the functions of OPR genes in cotton might be related to growth, development, hormone, and stresses. Expression patterns showed that GhOPRs were upregulated under salt treatment and repressed by polyethylene glycol 6000 (PEG6000). The expression patterns of GhOPRs were different in leaf, root, and stem under V. dahliae infection. GhOPR9 showed a higher expression level than other OPR genes in cotton root. The virus-induced gene silencing (VIGS) analysis suggested that knockdown of GhOPR9 could increase the susceptibility of cotton to V. dahliae infection. Furthermore, GhOPR9 also modulated the expressions of jasmonic acid (JA) pathway-regulated genes under the V. dahliae infection. Overall, our results provided the evolution and potential functions of the OPR genes in cotton. These findings suggested that GhOPR9 might play an important role in cotton resistance to V. dahliae.

Gene regulation in the white–opaque transition ofCandida albicans

1995 ◽  
Vol 73 (S1) ◽  
pp. 1049-1057 ◽  
Author(s):  
David R. Soll ◽  
Thyagarajan Srikantha ◽  
Brian Morrow ◽  
Anand Chandrasekhar ◽  
Klaus Schröppel ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Phenotypic Switching ◽  
Upstream Region ◽  
Specific Gene ◽  
Regulatory Sequences ◽  
Promoter Regions ◽  
Coordinate Regulation ◽  
Cis Acting ◽  
Ofcandida Albicans ◽  
Differential Transcription

Most strains of Candida albicans switch frequently and reversibly among a number of different phenotypes distinguishable by colony morphology. Previous experiments indicated that switching involved differential gene expression. Using the white–opaque transition as a model switching system, we have cloned two opaque-specific genes, PEP1 and OP4, and one white specific gene, WH11. Differential transcription of these genes suggested that switching involves the coordinate regulation of batteries of unlinked phase-specific genes. It has been demonstrated that the frequency of integration at phase specific loci is a function of the transcriptional state of the phase-specific genes. In addition, a functional dissection of the 5′-upstream region of the WH11 gene has identified two major domains containing cis-acting regulatory sequences that are involved in phase-specific transcription. Gel retardation experiments provide evidence for white phase-specific trans-acting factors which form complexes with both domains. The regulation of the switching event is discussed. Key words: Candida albicans, phenotypic switching, white–opaque transition, phase-specific genes, integrative transformation, promoter regions, WH11 gene.

scholarly journals Genome-wide investigation of malate dehydrogenase gene family in poplar (Populus trichocarpa) and their expression analysis under salt stress

2019 ◽  
Author(s):  
Xinghao Chen ◽  
Jun Zhang ◽  
Chao Zhang ◽  
Shijie Wang ◽  
Minsheng Yang
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Malate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Subcellular Location ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Malate dehydrogenase (MDH) is widely distributed in plants and animals, and plays an important role in many metabolic processes. However, there have been few studies on MDH genes in poplar. In this study, 16 MDH gene sequences were identified from the Populus trichocarpa genome and renamed according to their chromosomal locations. Based on phylogenetic analysis, the PtMDH genes were divided into five groups, and genes that grouped together all shared the same subcellular location and had similar sequence lengths, gene structures, and conserved motifs. Two pairs of tandem duplication events and three segmental duplication events involving five genes were identified from the 15 PtMDH genes located on the chromosomes. Each pair of genes had a Ka/Ks ratios <1, indicating that the MDH gene family of P. trichocarpa was purified during evolution. Based on the transcriptome data of P. trichocarpa under salt stress and qRT-PCR verification, the expression patterns of PtMDH genes under salt stress were analyzed. The results showed that most of the genes were upregulated under salt stress, indicating that they play a role in the response of poplar to salt stress. The PtmMDH1 gene can be used as an important salt-tolerant candidate gene for further investigations of molecular mechanisms. This study lays the foundation for functional analysis of MDH genes and genetic improvement in poplar.

scholarly journals The Transcriptional Repressor SmvR Is Important for Decreased Chlorhexidine Susceptibility in Enterobacter cloacae Complex

2019 ◽  
Vol 64 (1) ◽  
Author(s):  
François Guérin ◽  
François Gravey ◽  
Patrick Plésiat ◽  
Marion Aubourg ◽  
Racha Beyrouthy ◽  
...  
Keyword(s):  
Efflux Pump ◽  
Critical Role ◽  
Transcriptional Repressor ◽  
Enterobacter Cloacae ◽  
Major Facilitator Superfamily ◽  
Clinical Isolates ◽  
Bacterial Cells ◽  
Promoter Regions ◽  
Content Type ◽  
Major Facilitator

ABSTRACT Major facilitator superfamily (MFS) efflux pumps have been shown to be important for bacterial cells to cope with biocides such as chlorhexidine (CHX), a widely used molecule in hospital settings. In this work, we evaluated the role of two genes, smvA and smvR, in CHX resistance in Enterobacter cloacae complex (ECC). smvA encodes an MFS pump whereas smvR, located upstream of smvA, codes for a TetR-type transcriptional repressor. To this aim, we constructed corresponding deletion mutants from the ATCC 13047 strain (CHX MIC, 2 mg/liter) as well as strains overexpressing smvA or smvR in both ATCC 13047 and three clinical isolates exhibiting elevated CHX MICs (16 to 32 mg/liter). Determination of MICs revealed that smvA played a modest role in CHX resistance, in contrast to smvR that modulated the ability of ECC to survive in the presence of CHX. In clinical isolates, the overexpression of smvR significantly reduced MICs of CHX (2 to 8 mg/liter). Sequence analyses of smvR and promoter regions pointed out substitutions in conserved regions. Moreover, transcriptional studies revealed that SmvR acted as a repressor of smvA expression even if no quantitative correlation between the level of smvA mRNA and MICs of CHX could be observed. On the other hand, overproduction of smvA was able to complement the lack of the major resistance-nodulation-cell division (RND) superfamily efflux pump AcrB and restored resistance to ethidium bromide and acriflavine. Although SmvA could expel biocides such as CHX, other actors, whose expression is under SmvR control, should play a critical role in ECC.

scholarly journals B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis

Agronomy ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 23 ◽  
Author(s):  
Hanqi Jin ◽  
Mengge Xing ◽  
Chunmei Cai ◽  
Shuai Li
Keyword(s):  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Essential Information ◽  
Cis Acting ◽  
Arachis Duranensis ◽  
Gene Structures ◽  
Wild Peanut

B-box (BBX) proteins are important factors involved in plant growth and developmental regulation, and they have been identified in many species. However, information on the characteristics and transcription patterns of BBX genes in wild peanut are limited. In this study, we identified and characterized 24 BBX genes from a wild peanut, Arachis duranensis. Many characteristics were analyzed, including chromosomal locations, phylogenetic relationships, and gene structures. Arachis duranensis B-box (AdBBX) proteins were grouped into five classes based on the diversity of their conserved domains: I (3 genes), II (4 genes), III (4 genes), IV (9 genes), and V (4 genes). Fifteen distinct motifs were found in the 24 AdBBX proteins. Duplication analysis revealed the presence of two interchromosomal duplicated gene pairs, from group II and IV. In addition, 95 kinds of cis-acting elements were found in the genes’ promoter regions, 53 of which received putative functional predictions. The numbers and types of cis-acting elements varied among different AdBBX promoters, and, as a result, AdBBX genes exhibited distinct expression patterns in different tissues. Transcriptional profiling combined with synteny analysis suggests that AdBBX8 may be a key factor involved in flowering time regulation. Our study will provide essential information for further functional investigation of AdBBX genes.

scholarly journals Transcriptional response of Fusarium oxysporum and Neocosmospora solani challenged with amphotericin B or posaconazole

Microbiology ◽  
2020 ◽  
Vol 166 (10) ◽  
pp. 936-946 ◽  
Author(s):  
A. Castillo-Castañeda ◽  
S. J. Cañas-Duarte ◽  
M. Guevara-Suarez ◽  
J. Guarro ◽  
S. Restrepo ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Amphotericin B ◽  
Molecular Mechanisms ◽  
Transcriptional Response ◽  
Resistance Mechanisms ◽  
Transport Processes ◽  
Major Facilitator Superfamily ◽  
Ergosterol Synthesis ◽  
Transcriptional Changes ◽  
Major Facilitator

Some species of fusaria are well-known pathogens of humans, animals and plants. Fusarium oxysporum and Neocosmospora solani (formerly Fusarium solani) cause human infections that range from onychomycosis or keratitis to severe disseminated infections. In general, these infections are difficult to treat due to poor therapeutic responses in immunocompromised patients. Despite that, little is known about the molecular mechanisms and transcriptional changes responsible for the antifungal resistance in fusaria. To shed light on the transcriptional response to antifungals, we carried out the first reported high-throughput RNA-seq analysis for F. oxysporum and N. solani that had been exposed to amphotericin B (AMB) and posaconazole (PSC). We detected significant differences between the transcriptional profiles of the two species and we found that some oxidation-reduction, metabolic, cellular and transport processes were regulated differentially by both fungi. The same was found with several genes from the ergosterol synthesis, efflux pumps, oxidative stress response and membrane biosynthesis pathways. A significant up-regulation of the C-22 sterol desaturase (ERG5), the sterol 24-C-methyltransferase (ERG6) gene, the glutathione S-transferase (GST) gene and of several members of the major facilitator superfamily (MSF) was demonstrated in this study after treating F. oxysporum with AMB. These results offer a good overview of transcriptional changes after exposure to commonly used antifungals, highlights the genes that are related to resistance mechanisms of these fungi, which will be a valuable tool for identifying causes of failure of treatments.

scholarly journals Gene Structures, Classification, and Expression Models of theDREBTranscription Factor Subfamily inPopulus trichocarpa

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Yunlin Chen ◽  
Jingli Yang ◽  
Zhanchao Wang ◽  
Haizhen Zhang ◽  
Xuliang Mao ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Northern Analysis ◽  
Transcript Accumulation ◽  
Qrt Pcr ◽  
Duplication Events ◽  
Gene Structures ◽  
Responsive Element ◽  
Gene Subfamily

We identified 75 dehydration-responsive element-binding (DREB) protein genes inPopulus trichocarpa. We analyzed gene structures, phylogenies, domain duplications, genome localizations, and expression profiles. The phylogenic construction suggests that thePtrDREBgene subfamily can be classified broadly into six subtypes (DREBA-1 to A-6) inPopulus. The chromosomal localizations of thePtrDREBgenes indicated 18 segmental duplication events involving 36 genes and six redundantPtrDREBgenes were involved in tandem duplication events. There were fewer introns in thePtrDREBsubfamily. The motif composition ofPtrDREBwas highly conserved in the same subtype. We investigated expression profiles of this gene subfamily from different tissues and/or developmental stages. Sixteen genes present in the digital expression analysis had high levels of transcript accumulation. The microarray results suggest that 18 genes were upregulated. We further examined the stress responsiveness of 15 genes by qRT-PCR. A digital northern analysis showed that thePtrDREB17, 18,and32genes were highly induced in leaves under cold stress, and the same expression trends were shown by qRT-PCR. Taken together, these observations may lay the foundation for future functional analyses to unravel the biological roles ofPopulus’ DREBgenes.

The major facilitator superfamily member Slc37a2 is a novel macrophage- specific gene selectively expressed in obese white adipose tissue

2007 ◽  
Vol 293 (1) ◽  
pp. E110-E120 ◽  
Author(s):  
Ji Young Kim ◽  
Kristin Tillison ◽  
Shengli Zhou ◽  
Yu Wu ◽  
Cynthia M. Smas
Keyword(s):  
Metabolic Syndrome ◽  
Adipose Tissue ◽  
White Adipose Tissue ◽  
Mammalian Cells ◽  
Subcutaneous Fat ◽  
Ectopic Expression ◽  
Major Facilitator Superfamily ◽  
Specific Gene ◽  
Sugar Transporter ◽  
Major Facilitator

A marked degree of macrophage infiltration of white adipose tissue (WAT) occurs in obesity and may link excess adiposity with the chronic inflammatory state underlying metabolic syndrome and other comorbidities of obesity. Excess deposition of fat in the intra-abdominal vs. subcutaneous WAT depots is a key component of metabolic syndrome. Through construction and differential screening of a murine ob/ob WAT cDNA library, we identified Slc37a2, a novel sugar transporter of the major facilitator superfamily, to be twofold enriched in intra-abdominal vs. subcutaneous fat. We find Slc37a2 is a macrophage-enriched transcript. In murine tissues, Slc37a2 transcript is restricted to spleen, thymus, and obese WAT. It is also readily detected in the RAW264.7 macrophage cell line and increases 46-fold during macrophage differentiation of THP-1 human monocytes. Compared with wild-type mice, Slc37a2 transcript is increased epididymal ninefold in ob/ob WAT and assessment of expression of the macrophage marker emr1 indicated upregulation of Slc37a2 transcript in macrophages populating ob/ob WAT. Studies with PNGase F and tunicamycin reveal the Slc37a2 protein is posttranslationally modified by addition of N-linked glycans. Slc37a2 protein migrates as heterogeneous species of ∼50–75 kDa and its ectopic expression in mammalian cells results in the appearance of large intracellular vacuoles. We postulate that the function of this macrophage-specific putative sugar transporter is central to the metabolism of the macrophage population specifically present in obese WAT.

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