scholarly journals Genome-wide identification and expression analysis of glycine-rich protein genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

2019 ◽  
Author(s):  
Xiaonan Lu ◽  
Ming Gao ◽  
Yaxiong Cheng ◽  
Meilan Li ◽  
Xiaoyong XU
Keyword(s):  
Low Temperature ◽  
Chinese Cabbage ◽  
Molecular Mechanisms ◽  
Plant Stress ◽  
Evolutionary Relationship ◽  
Soft Rot ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Abnormal Expression ◽  
Glycine Rich Protein

Abstract Background Plant Glycine-rich proteins, a superfamily with a glycine-rich domain, play an important role in various stress such as low temperature, drought, high salt, and so on. Although the research of GRP genes has been reported in many plants, the GRP gene has seldom reported in Chinese cabbage so far. Research results made a guide to further understand the function of BrGRP genes in Chinese cabbage. Results In this study, a total of 141 glycine-rich protein genes were identified in Chinese cabbage by homology comparative analysis. A further prediction of physical and chemical characteristics revealed that 58.3% of BrGRPs were alkalines, 63.1% of BrGRPs were unstable, and 73.8% were hydrophilic. Conserved domain analysis showed that 110 BrGRPs contained 18 same conserved motifs, and could be classified into five main subclasses which the evolutionary relationship and gene structure may be conserved while the other 31 BrGRPs, including Bra014168 , Bra040002 , etc, may gain new functions or gradually lost gene functions according to the evolution process. These identified BrGRP genes were also located in ten chromosomes and three different subgenomes of Chinese cabbage, and 101 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the opened transcriptome data, we found that 138 BrGRP genes showed abnormal expression at high temperature, 108 BrGRP genes showed abnormal expression at low temperature, and 74 at drought stress, 47 at soft rot stress, while only 3 and 7 genes at ozone and salt stress, respectively. Further promoter motif analysis found that a large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE, were identified in their promoter regions, which were in correspondence with previous differential expression. In addition, some BrGRP genes were involved in multiple stresses suggested their broad-spectrum resistance. Conclusion A total of 141 GRP genes were identified in Chinese cabbage, which suggested their potential roles in plant stress response. But the molecular mechanisms by which BrGRP genes respond and resist biotic and abiotic stress remain unclear. These results may provide an important basis for the study of their function in Chinese cabbage.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Cold-Active β-Galactosidases: Insight into Cold Adaption Mechanisms and Biotechnological Exploitation

Marine Drugs ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 43
Author(s):  
Marco Mangiagalli ◽  
Marina Lotti
Keyword(s):  
Low Temperature ◽  
Molecular Mechanisms ◽  
Building Blocks ◽  
Cold Active ◽  
Cold Adaption ◽  
Glycosyl Donor ◽  
Pharmaceutical Industries ◽  
Biotechnological Processes ◽  
Hydrolysis Of ◽  
Insight Into

β-galactosidases (EC 3.2.1.23) catalyze the hydrolysis of β-galactosidic bonds in oligosaccharides and, under certain conditions, transfer a sugar moiety from a glycosyl donor to an acceptor. Cold-active β-galactosidases are identified in microorganisms endemic to permanently low-temperature environments. While mesophilic β-galactosidases are broadly studied and employed for biotechnological purposes, the cold-active enzymes are still scarcely explored, although they may prove very useful in biotechnological processes at low temperature. This review covers several issues related to cold-active β-galactosidases, including their classification, structure and molecular mechanisms of cold adaptation. Moreover, their applications are discussed, focusing on the production of lactose-free dairy products as well as on the valorization of cheese whey and the synthesis of glycosyl building blocks for the food, cosmetic and pharmaceutical industries.

scholarly journals Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 206
Author(s):  
Md Bashir Uddin ◽  
S.M. Bayejed Hossain ◽  
Mahmudul Hasan ◽  
Mohammad Nurul Alam ◽  
Mita Debnath ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Antimicrobial Resistance ◽  
In Silico ◽  
Salmonella Enterica ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Genetic Relationships ◽  
Evolutionary Relationship ◽  
Salmonella Spp ◽  
Gram Negative

Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.

Molecular Insights into Beneficial Effects of Tea-Plant Growth and Selenium Enrichment by Herbaspirillum camelliae

2021 ◽  
pp. 37-51
Author(s):  
Wei Cheng ◽  
Xuejing Yu ◽  
Xingguo Wang
Keyword(s):  
Plant Growth ◽  
Molecular Mechanisms ◽  
Acc Deaminase ◽  
Nitrogen Sources ◽  
Endophytic Bacterium ◽  
Tea Plant ◽  
Nitrogen Fixing ◽  
Biotic And Abiotic Stress ◽  
Bacterial Strains ◽  
Secretion Systems

Herbaspirillum camelliae WT00C, as a tea-plant endophytic bacterium, not only colonizes specifically in tea plants but also promotes tea-plant growth and selenium enrichment. Different from diazotrophic endophytes H. seropedicae, H. frisingense and H. rubrisubalbicans, H. camelliae WT00C does not display nitrogen-fixing activity. To understand the molecular mechanisms of promoting the growth of tea plant and Se-enrichment, we sequenced and annotated the genome of H. camelliae WT00C. The results showed that the genome was composed of 6,079,821 base pairs with a total of 5,537 genes. The genomic survey also revealed that H. camelliae WT00C was a multifunctional bacterium metabolizing a variety of carbon and nitrogen sources and defending against biotic and abiotic stress. Although this bacterium did not have intact nitrogen-fixing genes, its genome held the genes responsible for indole-3-acetic acid (IAA) biosynthesis, 1-aminocyclopropane-1-carboxylate (ACC) deamination, siderophore synthesis, ammonia formation, urea metabolism, glutathione and selenocompound metabolisms. Biosynthesis of IAA, siderophore, ammonia, urea and ACC deaminase could explain why two bacterial strains promote tea-plant growth and development. Selenocompound metabolism in this bacterium might also benefit tea-plant growth and Se-enrichment. In addition, the genome of H. camelliae also contained a multitude of protein secretion systems T1SS, T3SS, T4SS and T6SS, in which T4SS did not exhibit in other members of the genus Herbaspirillum.

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

2021 ◽  
Author(s):  
Qi Ai ◽  
Wenqiu Pan ◽  
Yan Zeng ◽  
Yihan Li ◽  
Licao Cui
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Zinc Finger ◽  
Molecular Breeding ◽  
Animal Feed ◽  
Expression Profiles ◽  
Exome Capture ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Developmental Processes

Abstract Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

scholarly journals A class III WRKY transcription factor in sugarcane was involved in biotic and abiotic stress responses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Dongjiao Wang ◽  
Ling Wang ◽  
Weihua Su ◽  
Yongjuan Ren ◽  
Chuihuai You ◽  
...  
Keyword(s):  
Stress Responses ◽  
Transcriptional Activation ◽  
Abiotic Factors ◽  
Plant Stress ◽  
Bacterial Pathogen ◽  
Wrky Transcription Factor ◽  
Expression Level ◽  
Class Iii ◽  
Biotic And Abiotic Stress ◽  
Sporisorium Scitamineum

AbstractWRKY transcription factors play significant roles in plant stress responses. In this study, a class III WRKY gene ScWRKY5, was successfully isolated from sugarcane variety ROC22. The ScWRKY5 was a nucleus protein with transcriptional activation activity. The ScWRKY5 gene was constitutively expressed in all the sugarcane tissues, with the highest expression level in the stem epidermis and the lowest in the root. After inoculation with Sporisorium scitamineum for 1 d, the expression level of ScWRKY5 was significantly increased in two smut-resistant varieties (YZ01-1413 and LC05-136), while it was decreased in three smut-susceptible varieties (ROC22, YZ03-103, and FN40). Besides, the expression level of ScWRKY5 was increased by the plant hormones salicylic acid (SA) and abscisic acid (ABA), as well as the abiotic factors polyethylene glycol (PEG) and sodium chloride (NaCl). Transient overexpression of the ScWRKY5 gene enhanced the resistance of Nicotiana benthamiana to the tobacco bacterial pathogen Ralstonia solanacearum, however the transiently overexpressed N. benthamiana was more sensitive to the tobacco fungal pathogen Fusarium solani var. coeruleum. These results provide a reference for further research on the resistance function of sugarcane WRKY genes.

Control on Soft Rot of Chinese Cabbage Using Harpin Protein

2011 ◽  
Vol 183-185 ◽  
pp. 2078-2081
Author(s):  
Tian Lei Qiu ◽  
Min Wang ◽  
Xiao Hong Sun ◽  
Mei Lin Han ◽  
Xu Ming Wang
Keyword(s):  
Chinese Cabbage ◽  
Soft Rot ◽  
Coli Strain ◽  
Economic Losses ◽  
Common Disease ◽  
Control Effect ◽  
Protein Preparation ◽  
E Coli ◽  
Wettable Powder ◽  
Harpin Protein

Soft rot of Chinese cabbage is a common disease that causes serious damage and economic losses. In this study, the control on soft rot of growing and postharvest Chinese cabbage was carried out, using Harpin protein which was the expressed product of a recombinant E. coli strain. The experimental results indicate that Harpin protein preparation containing 3% pure protein powder and 97% wettable powder of Bacillus Thuringiensis (Bt), could effectively control soft rot of Chinese cabbage. The control effect on soft rot reached as high as 90% for growing Chinese cabbage using Harpin protein at 6-10mg/m2 of dosage, and the control effect reached approximately 75% for postharvest Chinese cabbage. Harpin protein stored for 6 months at 20-25 0C had the similarly biological activity with the newly prepared protein.

scholarly journals Combating stress: the interplay between hormone signaling and autophagy in plants

2019 ◽  
Vol 71 (5) ◽  
pp. 1723-1733 ◽  
Author(s):  
Ching-Yi Liao ◽  
Diane C Bassham
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
Plant Stress ◽  
Stress Conditions ◽  
Hormone Signaling ◽  
Hormone Synthesis ◽  
Energy Sensor ◽  
Sensor Kinases ◽  
Plant Stress Responses ◽  
Cellular Components

Abstract Autophagy is a conserved recycling process in which cellular components are delivered to and degraded in the vacuole/lysosome for reuse. In plants, it assists in responding to dynamic environmental conditions and maintaining metabolite homeostasis under normal or stress conditions. Under stress, autophagy is activated to remove damaged components and to recycle nutrients for survival, and the energy sensor kinases target of rapamycin (TOR) and SNF-related kinase 1 (SnRK1) are key to this activation. Here, we discuss accumulating evidence that hormone signaling plays critical roles in regulating autophagy and plant stress responses, although the molecular mechanisms by which this occurs are often not clear. Several hormones have been shown to regulate TOR activity during stress, in turn controlling autophagy. Hormone signaling can also regulate autophagy gene expression, while, reciprocally, autophagy can regulate hormone synthesis and signaling pathways. We highlight how the interplay between major energy sensors, plant hormones, and autophagy under abiotic and biotic stress conditions can assist in plant stress tolerance.

Pathogenic fungal protein-induced resistance and its effects on vegetable diseases

2017 ◽  
Vol 155 (7) ◽  
pp. 1069-1081 ◽  
Author(s):  
T.-C. LIN ◽  
C.-L. LIN ◽  
W.-C. CHUNG ◽  
K.-R. CHUNG ◽  
J.-W. HUANG
Keyword(s):  
Chinese Cabbage ◽  
Fungal Pathogens ◽  
Plant Defence ◽  
Black Spot ◽  
Sweet Pepper ◽  
Alternaria Brassicicola ◽  
Biotic And Abiotic Stress ◽  
Promote Plant Growth ◽  
Test Plants ◽  
Reduce Disease Severity

SUMMARYPlant defence systems can be induced by biotic and abiotic stress. Experiments were undertaken to explore the feasibility of different fungal proteins for the reduction of vegetable diseases. Total proteins purified from three soil-borne and five foliar fungal pathogens had no fungistatic effects nor did they trigger hypersensitive reactions on test plants. The abilities to promote plant growth and to reduce disease severity varied among test proteins and plants. Depending on test proteins, experiments have demonstrated that exogenous application of fungal proteins could reduce Alternaria brassicicola-induced black spot severity on cabbage, Colletotrichum spp.-induced anthracnose on Chinese cabbage and cucumber, Rhizoctonia solani-induced damping-off on sweet pepper and Chinese cabbage, and powdery mildew on cucumber seedlings. An Alternariaprotein effector 1 (Ape1)-coding gene was cloned from two Alternaria spp. and expressed in Escherichia coli. The expressed Ape1 reduced anthracnose incidence on cucumber leaves, indicating that Ape1 was the primary activator in the crude protein extracts responsible for disease reduction. Application of Alternaria proteins onto Chinese cabbage seedlings caused an increase of phenylalanine ammonia lyase and peroxidase activities in treated seedlings, which may have played a role in host defence.

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