RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

Endodormancy release and the fulfillment of the chilling requirement (CR) are critical physiological processes that enable uniform blooming in fruit tree species, including apple (Malus ×domestica). However, the molecular mechanisms underlying these traits have not been fully characterized. The objective of this study was to identify potential master regulators of endodormancy release and the CR in apple. We conducted RNA-Sequencing (RNA-seq) analyses and narrowed down the number of candidates among the differentially expressed genes (DEGs) based on the following two strict screening criteria: 1) the gene must be differentially expressed between endodormant and ecodormant buds under different environmental conditions and 2) the gene must exhibit chill unit (CU)–correlated expression. The results of our cluster analysis suggested that global expression patterns varied between field-grown buds and continuously chilled buds, even though they were exposed to similar amounts of chilling and were expected to have a similar dormancy status. Consequently, our strict selection strategy resulted in narrowing down the number of possible candidates and identified the DEGs strongly associated with the transition between dormancy stages. The genes included four transcription factor genes, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS C (FLC)-LIKE, APETALLA2 (AP2)/ETHYLENE-RESPONSIVE 113 (ERF113), and MYC2. Their expressions were upregulated during endodormancy release, and were correlated with the CU, suggesting that these transcription factors are closely associated with chilling-mediated endodormancy release in apple.

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Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20102391 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2391 ◽

Cited By ~ 3

Author(s):

Jiayang Xu ◽

Qiansi Chen ◽

Pingping Liu ◽

Wei Jia ◽

Zheng Chen ◽

...

Keyword(s):

Salinity Stress ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Crop Yields ◽

Antioxidant Activities ◽

Expression Patterns ◽

Differentially Expressed ◽

Alkali Stress ◽

Rna Seq ◽

Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

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Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽

10.1182/blood.v120.21.4582.4582 ◽

2012 ◽

Vol 120 (21) ◽

pp. 4582-4582

Author(s):

Wei Liao ◽

Gwen Jordaan ◽

Artur Jaroszewicz ◽

Matteo Pellegrini ◽

Sanjai Sharma

Keyword(s):

B Cells ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Fold Change ◽

Differentially Expressed ◽

Pcr Analysis ◽

Sequencing Analysis ◽

Rna Seq ◽

Mrna Isoforms ◽

Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

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Deep RNA sequencing analysis of syncytialization-related genes during BeWo cell fusion

Reproduction ◽

10.1530/rep-16-0343 ◽

2017 ◽

Vol 153 (1) ◽

pp. 35-48 ◽

Cited By ~ 4

Author(s):

Ru Zheng ◽

Yue Li ◽

Huiying Sun ◽

Xiaoyin Lu ◽

Bao-Fa Sun ◽

...

Keyword(s):

Rna Sequencing ◽

Cell Fate ◽

Cell Fusion ◽

Mapk Pathway ◽

Differentially Expressed ◽

Cell Junction ◽

Bewo Cell ◽

Sequencing Analysis ◽

Rna Seq ◽

Bewo Cells

The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethyl sulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h were sequenced. We detected 28,633 expressed genes and identified 1902 differentially expressed genes (DEGs) after FSK treatment for 24 and 48 h. Among the 1902 DEGs, 461 were increased and 395 were decreased at 24 h, whereas 879 were upregulated and 763 were downregulated at 48 h. When the 856 DEGs identified at 24 h were traced individually at 48 h, they separated into 6 dynamic patterns via a K-means algorithm, and most were enriched in down–even and up–even patterns. Moreover, the gene ontology (GO) terms syncytium formation, cell junction assembly, cell fate commitment, calcium ion transport, regulation of epithelial cell differentiation and cell morphogenesis involved in differentiation were clustered, and the MAPK pathway was most significantly regulated. Analyses of alternative splicing isoforms detected 123,200 isoforms, of which 1376 were differentially expressed. The present deep analysis of the RNA-Seq data of BeWo cell fusion provides important clues for understanding the mechanisms underlying human STB formation.

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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

10.20944/preprints202010.0158.v1 ◽

2020 ◽

Author(s):

Thiago Mateus Rosa-Santos ◽

Renan Gonçalves da Silva ◽

Poornasree Kumar ◽

Pratibha Kottapalli ◽

Chiquito Crasto ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Aluminum Tolerance ◽

Differentially Expressed ◽

Rna Seq ◽

Aluminum Stress ◽

Physiological Processes ◽

Aluminum Ions ◽

Detoxification Mechanism ◽

Genomic Studies

Sugarcane is an important sugar-source crop. As any other plant, it can be exposed to several abiotic stress conditions. Though some metals contribute to critical physiological processes in plants, the presence of aluminum ions (Al3+) can be very toxic. In order to develop plants that flourish in acidic soils, it is critical to gain insights into the molecular mechanisms of sugarcane response to aluminum stress. To determine the genes involved in sugarcane response to aluminum stress we generated 372 million paired-end RNA sequencing reads, from roots of CTC-2 and RB855453 two contrasting cultivars. Data normalization resulted in 162,161 contigs and 97,335 trinity genes. After the read cutoff, the differentially expressed genes were 4,858 in CTC-2 and 1,307 in the RB855453, Treatment Vs Control, respectively. The differentially expressed genes were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and down regulated in RB855453 (sensitive cultivar). Here, we present the first root-transcriptome of sugarcane under aluminum stress. The results and conclusions of this study provide a valuable resource for future genetic and genomic studies in sugarcane. This transcriptome analysis points out that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with the lateral root formation and activation of redox enzymes. Following our results, we present here, a hypothetical model for the aluminum tolerance in CTC-2 cultivar.

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Comparative Transcriptome Analysis of a Fan-shaped Inflorescence in Pineapple Using RNA-seq

10.21203/rs.3.rs-52110/v1 ◽

2020 ◽

Author(s):

Tao Xie ◽

Zhiquan Cai ◽

Aiping Luan ◽

Wei Zhang ◽

Jing Wu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Expression Patterns ◽

Soluble Sugar ◽

Differentially Expressed ◽

Soluble Solids ◽

Pcr Analysis ◽

Rna Seq ◽

Stem Apex ◽

Inflorescence Axis ◽

Flower Stem

Abstract Background: Pineapple plant usually has a capitulum. However, a fan-shaped inflorescence was evolved in an exceptional material, having multiple crown buds. In order to reveal the molecular mechanisms of the formation of the fan-shaped inflorescence, fruit traits and the transcriptional differences between a fan-shaped inflorescence (FI) and a capitulum inflorescence (CI) pineapples were analyzed in the three tissues, i.e., the flower stem apex (FIs and CIs), the base of the inflorescence (FIb and CIb), and the inflorescence axis (FIa and CIa).Results: Except for a clear differentiation of inflorescence morphology, no significant differences in the structure of inflorescence organs and the main nutritional components (soluble solids, soluble sugar, titratable acid, and VC) in fruits were found between the two pineapples. Between the fan- and capitulum-shaped inflorescences, a total of 5370 differentially expressed genes (DEGs) were identified across the three tissues; and 3142, 2526 and 2255 DEGs were found in the flower stem apex, the base of the inflorescence, and the inflorescence axis, respectively. Of these genes, there were 489 overlapping DEGs in all three tissue comparisons. In addition, 5769 DEGs were identified between different tissues within each pineapple. Functional analysis indicated between the two pineapples that 444 transcription factors (TFs) and 206 inflorescence development related genes (IDGs) were differentially expressed in at least one tissue comparison, while 45 TFs and 21 IDGs were overlapped across the 3 tissues. Among the 489 overlapping DEGs in the 3 tissue comparisons between the two pineapples, excluding the IDGs and TFs, 80 of them revealed a higher percentage of involvement in the biological processes relating to response to auxin, and reproductive processes. RNA-seq value and real-time quantitative PCR analysis exhibited the same gene expression patterns in the three tissues. Conclusions: Our result provided novel cues for understanding the molecular mechanisms of the formation of fan-shaped inflorescence in pineapple, making a valuable resource for the study of plant breeding and the speciation of the pineapples.

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PSII-11 RNA sequencing analysis reveals differentially expressed genes and novel upstream transcriptional regulators in porcine longissimus dorsi muscle affected by dietary lysine restriction

Journal of Animal Science ◽

10.1093/jas/skz258.474 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 233-233

Author(s):

Ying Wang ◽

Huaijun Zhou ◽

Shengfa F Liao

Keyword(s):

Protein Synthesis ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Muscle Protein ◽

Transcriptional Regulators ◽

Growing Pigs ◽

Differentially Expressed ◽

Longissimus Dorsi ◽

Sequencing Analysis ◽

Rna Seq

Abstract The objective of this research was to investigate the effects of dietary lysine restriction on the global gene expression of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (Diet I: a lysine-deficient diet; Diet II: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, muscle samples were collected from longissimus dorsi of individual pigs (approximately 2 g/each). The total RNA isolated was used to prepare cDNA library for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). Sixty-nine genes were found differentially expressed (Benjamin-Hochberg corrected P < 0.05) in Diet I vs. Diet II pigs, of which 29 genes were down-regulated (Log₂ fold change (FC) < - 0.58) and 40 genes were up-regulated (Log₂ FC > 0.58). Gene ontology (GO) analysis of these DEGs for functional annotation using DAVID found a total of 36 GO terms. The significantly enriched terms (Benjamin-Hochberg corrected P < 0.05) are associated with biological processes that include acute-phase response, platelet activation, and protein polymerization, and Molecular Functions that include serine-type endopeptidase inhibitor activity, small molecule binding, heme binding, and oxidoreductase activity. In addition, Ingenuity Pathway Analysis predicted some upstream transcriptional regulators that regulate several sets of DEGs. For example, lysine restriction may lead inhibition of insulin, EIF2AK4 (an eIF2α activator), and MYC (a transcript elongation factor), which are associated with the regulation of protein synthesis. It may also lead activation of STAT3 and HNF1A, which regulate cell movement and fatty acid metabolism, respectively. In summary, these novel results showed that dietary lysine restriction may compromise pig muscle protein synthesis through the aforementioned transcriptional regulators and their affected genes.

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Compatative Transcriptome Analysis Reveals Sesquiterpene Biosynthesis among 1-, 2- and 3-year Old Atractylodes Chinensis

10.21203/rs.3.rs-272708/v1 ◽

2021 ◽

Author(s):

Jianhua Zhao ◽

Chengzhen Sun ◽

Shanshan Ma ◽

Jinshuang Zheng ◽

Xin Du ◽

...

Keyword(s):

Rna Sequencing ◽

Transcriptome Analysis ◽

High Performance ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Bioactive Compound ◽

Pcr Analysis ◽

Squalene Epoxidase ◽

Sequencing Analysis ◽

Qrt Pcr

Abstract Background: Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atrctylodin, a sesquiterpenoids. High-performance liquid chromatography (HPLC) analysis demonstrated that atrctylodin was most abundant in 3-year old A. chinensis rhizomes, compared with those from 1-year and 2-year-old plants, however, the molecular mechanisms underlying accumulation of atrctylodin in rhizomes are poorly understood. Results: In this study, we characterized the transcriptomes from 1-, 2, and 3-year old (Y1, Y2, and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 205 and 226 unigenes encoding the enzyme genes in the mevalonate (MVA) and methylerythritol phosphate (MEP) sesquiterpenoid biosynthesis pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven genes key genes encoding factors involved in the sesquiterpene biosynthetic pathway, as well as in pigment, amino acid, hormone, and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of samples from different ages revealed 52 genes related to sesquiterpenoids biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3, and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase, squalene-hopene cyclase, squalene epoxidase and dammarenediol II synthase. These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion: The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenes in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.

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Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Plants ◽

10.3390/plants9101335 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1335

Author(s):

Hsueh-Yuan Chang ◽

Cindy B. S. Tong

Keyword(s):

Cell Wall ◽

Fruit Ripening ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Differentially Expressed ◽

Rna Seq ◽

Phenotypic Differences ◽

Genes Encoding ◽

A Cell ◽

Phenotypic Groups

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

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Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis

BMC Plant Biology ◽

10.1186/s12870-021-03131-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jianhua Zhao ◽

Chengzhen Sun ◽

Fengyu Shi ◽

Shanshan Ma ◽

Jinshuang Zheng ◽

...

Keyword(s):

Rna Sequencing ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Pcr Analysis ◽

Squalene Epoxidase ◽

Sequencing Analysis ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis ◽

Qrt Pcr

Abstract Background Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atractylodin, a sesquiterpenoid. High-performance liquid chromatography (HPLC) analysis demonstrated that atractylodin was most abundant in 3-year old A. chinensis rhizome, compared with those from 1- and 2-year old rhizomes, however, the molecular mechanisms underlying accumulation of atractylodin in rhizomes are poorly understood. Results In this study, we characterized the transcriptomes from rhizomes of 1-, 2- and 3-year old (Y1, Y2 and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 240, 169 and 131 unigenes encoding the enzyme genes in the mevalonate (MVA), methylerythritol phosphate (MEP), sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven key gene encoding factors involved in the sesquiterpenoid and triterpenoid biosynthetic pathway, as well as in pigment, amino acid, hormone and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of rhizomes from different ages revealed 52 genes related to sesquiterpenoid and triterpenoid biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3 and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase (SS), squalene-hopene cyclase (SHC), squalene epoxidase (SE) and dammarenediol II synthase (DS). These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenoid in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.

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Genome-Wide RNA Sequencing Analysis of Quorum Sensing-Controlled Regulons in the Plant-Associated Burkholderia glumae PG1 Strain

Applied and Environmental Microbiology ◽

10.1128/aem.01043-15 ◽

2015 ◽

Vol 81 (23) ◽

pp. 7993-8007 ◽

Cited By ~ 25

Author(s):

Rong Gao ◽

Dagmar Krysciak ◽

Katrin Petersen ◽

Christian Utpatel ◽

Andreas Knapp ◽

...

Keyword(s):

Quorum Sensing ◽

Rna Sequencing ◽

Differentially Expressed ◽

Phenotypic Characterization ◽

Regulation System ◽

Sequencing Analysis ◽

Rna Seq ◽

Burkholderia Glumae ◽

Content Type ◽

Genome Wide

ABSTRACTBurkholderia glumaePG1 is a soil-associated motile plant-pathogenic bacterium possessing a cell density-dependent regulation system called quorum sensing (QS). Its genome contains three genes, here designatedbgaI1tobgaI3, encoding distinct autoinducer-1 (AI-1) synthases, which are capable of synthesizing QS signaling molecules. Here, we report on the construction ofB. glumaePG1 ΔbgaI1, ΔbgaI2, and ΔbgaI3mutants, their phenotypic characterization, and genome-wide transcriptome analysis using RNA sequencing (RNA-seq) technology. Knockout of each of thesebgaIgenes resulted in strongly decreased motility, reduced extracellular lipase activity, a reduced ability to cause plant tissue maceration, and decreased pathogenicity. RNA-seq analysis of all threeB. glumaePG1 AI-1 synthase mutants performed in the transition from exponential to stationary growth phase revealed differential expression of a significant number of predicted genes. In comparison with the levels of gene expression by wild-type strainB. glumaePG1, 481 genes were differentially expressed in the ΔbgaI1mutant, 213 were differentially expressed in the ΔbgaI2mutant, and 367 were differentially expressed in the ΔbgaI3mutant. Interestingly, only a minor set of 78 genes was coregulated in all three mutants. The majority of the QS-regulated genes were linked to metabolic activities, and the most pronounced regulation was observed for genes involved in rhamnolipid and Flp pilus biosynthesis and the type VI secretion system and genes linked to a clustered regularly interspaced short palindromic repeat (CRISPR)-casgene cluster.

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