scholarly journals Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhiqiang Du ◽  
Jeniece Regan ◽  
Elizabeth Bartom ◽  
Wei-Sheng Wu ◽  
Li Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Regulation Of Transcription ◽  
Interacting Proteins ◽  
Environmental Stress Response ◽  
Key Factors ◽  
Cellular Functions ◽  
Beneficial Effects ◽  
Genome Wide ◽  
Genes Encoding ◽  
A Subunit

AbstractTranscriptional regulators are prevalent among identified prions in Saccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription. We show here that the prion ([SWI+]) and mutant (swi1∆) forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI+] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI+] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI+] cells. Interestingly, swi1∆ and [SWI+] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, are significantly reduced in swi1∆ cells. Although both swi1∆ and [SWI+] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different between swi1∆ and [SWI+] cells—stress-inducible ESR (iESR) are repressed by [SWI+] but unchanged by swi1∆ while stress-repressible ESR (rESR) are induced by [SWI+] but repressed by swi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI+] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.

scholarly journals Genome-Wide Identification of Francisella tularensis Virulence Determinants

2007 ◽  
Vol 75 (6) ◽  
pp. 3089-3101 ◽  
Author(s):  
Jingliang Su ◽  
Jun Yang ◽  
Daimin Zhao ◽  
Thomas H. Kawula ◽  
Jeffrey A. Banas ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Stress Responses ◽  
Small Subset ◽  
Virulence Determinants ◽  
Genome Wide ◽  
Genes Encoding ◽  
Capsule Locus ◽  
Life Threatening ◽  
Transposon Mutants ◽  
Schu S4

ABSTRACT Francisella tularensis is a gram-negative pathogen that causes life-threatening infections in humans and has potential for use as a biological weapon. The genetic basis of the F. tularensis virulence is poorly understood. This study screened a total of 3,936 transposon mutants of the live vaccine strain for infection in a mouse model of respiratory tularemia by signature-tagged mutagenesis. We identified 341 mutants attenuated for infection in the lungs. The transposon disruptions were mapped to 95 different genes, virtually all of which are also present in the genomes of other F. tularensis strains, including human pathogenic F. tularensis strain Schu S4. A small subset of these attenuated mutants carried insertions in the genes encoding previously known virulence factors, but the majority of the identified genes have not been previously linked to F. tularensis virulence. Among these are genes encoding putative membrane proteins, proteins associated with stress responses, metabolic proteins, transporter proteins, and proteins with unknown functions. Several attenuated mutants contained disruptions in a putative capsule locus which partially resembles the poly-γ-glutamate capsule biosynthesis locus of Bacillus anthracis, the anthrax agent. Deletional mutation analysis confirmed that this locus is essential for F. tularensis virulence.

scholarly journals Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Qinglong Dong ◽  
Ke Mao ◽  
Dingyue Duan ◽  
Shuang Zhao ◽  
Yanpeng Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Binding Proteins ◽  
Genome Wide ◽  
Genes Encoding ◽  
Fk506 Binding Proteins

scholarly journals Genome-Wide Characterization of Peptidyl-Prolyl Cis-Trans Isomerases in Penicillium and Their Regulation By Salt Stress in a Halotolerant P. Oxalicum

2021 ◽  
Author(s):  
Mangaljeet Singh ◽  
Kirandeep Kaur ◽  
Avinash Sharma ◽  
Rajvir Kaur ◽  
Dimple Joshi ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Families ◽  
Peptide Bond ◽  
Penicillium Oxalicum ◽  
Cellular Functions ◽  
Ppiase Activity ◽  
Genome Wide ◽  
Genes Encoding ◽  
Penicillium Spp

Abstract Peptidyl-prolyl cis-trans isomerases (PPIases) are the only class of enzymes capable of cis-trans isomerization of the prolyl peptide bond. The PPIases, comprising of different families viz., cyclophilins, FK506-binding proteins (FKBPs), parvulins and protein phosphatase 2A phosphatase activators (PTPAs), play essential roles in different cellular processes. Though PPIase gene families have been characterized in different organisms, information regarding these proteins lacks in Penicillium species, which are commercially an important fungi group. In this study, we carried out genome-wide analysis of PPIases in different Penicillium spp. and investigated their regulation by salt stress in a halotolerant strain of Penicillium oxalicum. These analyses revealed that the number of genes encoding cyclophilins, FKBPs, parvulins and PTPAs in Penicillium spp. varies between 7-11, 2-5, 1-2, and 1-2, respectively. The halotolerant P. oxalicum depicted significant enhancement in the mycelial PPIase activity in the presence of 15% NaCl, thus, highlighting the role of these enzymes in salt stress adaptation. The PPIase activity in P. oxalicum was associated with the expression of PoxCYP18, PoxCYP23, PoxCYP41, PoxFKBP12-2, and PoxFKBP52 genes. Characterization of PPIases in Penicillium spp. will provide an important database for understanding their cellular functions and might facilitate their applications in industrial processes through biotechnological interventions.

Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses

2018 ◽  
Vol 45 (6) ◽  
pp. 2653-2669 ◽  
Author(s):  
Adwaita Prasad Parida ◽  
Utkarsh Raghuvanshi ◽  
Amit Pareek ◽  
Vijendra Singh ◽  
Rahul Kumar ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Fruit Development ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Genes Encoding

scholarly journals Identification and Characterization of Elf1, a Conserved Transcription Elongation Factor in Saccharomyces cerevisiae

2005 ◽  
Vol 25 (22) ◽  
pp. 10122-10135 ◽  
Author(s):  
Donald Prather ◽  
Nevan J. Krogan ◽  
Andrew Emili ◽  
Jack F. Greenblatt ◽  
Fred Winston
Keyword(s):  
Synthetic Lethality ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Regulation Of Transcription ◽  
Elongation Factors ◽  
Genome Wide ◽  
Genes Encoding ◽  
Active Transcription ◽  
Identification And Characterization

ABSTRACT In order to identify previously unknown transcription elongation factors, a genetic screen was carried out to identify mutations that cause lethality when combined with mutations in the genes encoding the elongation factors TFIIS and Spt6. This screen identified a mutation in YKL160W, hereafter named ELF1 (elongation factor 1). Further analysis identified synthetic lethality between an elf1Δ mutation and mutations in genes encoding several known elongation factors, including Spt4, Spt5, Spt6, and members of the Paf1 complex. Genome-wide synthetic lethality studies confirmed that elf1Δ specifically interacts with mutations in genes affecting transcription elongation. Chromatin immunoprecipitation experiments show that Elf1 is cotranscriptionally recruited over actively transcribed regions and that this association is partially dependent on Spt4 and Spt6. Analysis of elf1Δ mutants suggests a role for this factor in maintaining proper chromatin structure in regions of active transcription. Finally, purification of Elf1 suggests an association with casein kinase II, previously implicated in roles in transcription. Together, these results suggest an important role for Elf1 in the regulation of transcription elongation.

scholarly journals Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms

2021 ◽  
Author(s):  
Evan S Forsythe ◽  
Alissa M Williams ◽  
Daniel B Sloan
Keyword(s):  
Nuclear Genome ◽  
Protein Translation ◽  
Nuclear Genes ◽  
Sequence Evolution ◽  
Cellular Functions ◽  
Transmission Modes ◽  
Chloroplast Genomes ◽  
Genome Wide ◽  
Genes Encoding ◽  
Phylogenomic Analyses

Abstract Nuclear and plastid (chloroplast) genomes experience different mutation rates, levels of selection, and transmission modes, yet key cellular functions depend on their coordinated interactions. Functionally related proteins often show correlated changes in rates of sequence evolution across a phylogeny (evolutionary rate covariation or ERC), offering a means to detect previously unidentified suites of coevolving and cofunctional genes. We performed phylogenomic analyses across angiosperm diversity, scanning the nuclear genome for genes that exhibit ERC with plastid genes. As expected, the strongest hits were highly enriched for genes encoding plastid-targeted proteins, providing evidence that cytonuclear interactions affect rates of molecular evolution at genome-wide scales. Many identified nuclear genes functioned in post-transcriptional regulation and the maintenance of protein homeostasis (proteostasis), including protein translation (in both the plastid and cytosol), import, quality control and turnover. We also identified nuclear genes that exhibit strong signatures of coevolution with the plastid genome, but their encoded proteins lack organellar-targeting annotations, making them candidates for having previously undescribed roles in plastids. In sum, our genome-wide analyses reveal that plastid-nuclear coevolution extends beyond the intimate molecular interactions within chloroplast enzyme complexes and may be driven by frequent rewiring of the machinery responsible for maintenance of plastid proteostasis in angiosperms.

Recent insights into regulation of transcription by RNA polymerase III and the cellular functions of its transcripts

2011 ◽  
Vol 392 (5) ◽  
Author(s):  
Tatyana V. Nikitina ◽  
Lyudmila I. Tischenko ◽  
Wolfgang A. Schulz
Keyword(s):  
Rna Polymerase ◽  
Stress Responses ◽  
Rna Polymerase Iii ◽  
Cell Types ◽  
Regulation Of Transcription ◽  
Class Iii ◽  
Cellular Functions ◽  
U6 Snrna ◽  
Polymerase Iii ◽  
Pol Iii

AbstractThe products of transcription by the multisubunit enzyme RNA polymerase III (Pol III), such as 5S rRNA, tRNAs, U6 snRNA, are important for cell growth, proliferation and differentiation. The known range of the Pol III transcriptome has expanded over recent years, and novel functions of the newly discovered and already well known transcripts have been identified, including regulation of stress responses and apoptosis. Furthermore, transcription by Pol III has turned out to be strongly regulated, differing between diverse class III genes, among cell types and under stress conditions. The mechanisms involved in regulation of Pol III transcription are being elucidated and disturbances in that regulation have been implicated in various diseases, including cancer. This review summarizes the novel data on the regulation of RNA polymerase III transcription, including epigenetic and gene specific mechanisms and outlines recent insights into the cellular functions of the Pol III transcriptome, in particular of SINE RNAs.

scholarly journals Genome-Wide Mapping Reveals Complex Regulatory Activities of BfmR in Pseudomonas aeruginosa

2021 ◽  
Vol 9 (3) ◽  
pp. 485
Author(s):  
Ke Fan ◽  
Qiao Cao ◽  
Lefu Lan
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Chromatin Immunoprecipitation ◽  
Biofilm Formation ◽  
High Throughput Sequencing ◽  
Response Regulator ◽  
Cellular Functions ◽  
Genome Wide ◽  
Component Systems ◽  
Genes Encoding ◽  
Two Component Systems

BfmR is a response regulator that modulates diverse pathogenic phenotypes and induces an acute-to-chronic virulence switch in Pseudomonas aeruginosa, an important human pathogen causing serious nosocomial infections. However, the mechanisms of action of BfmR remain largely unknown. Here, using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we showed that 174 chromosomal regions of P. aeruginosa MPAO1 genome were highly enriched by coimmunoprecipitation with a C-terminal Flag-tagged BfmR. Integration of these data with global transcriptome analyses revealed that 172 genes in 106 predicted transcription units are potential targets for BfmR. We determined that BfmR binds to and modulates the promoter activity of genes encoding transcriptional regulators CzcR, ExsA, and PhoB. Intriguingly, BfmR bound to the promoters of a number of genes belong to either CzcR or PhoB regulon, or both, indicating that CzcRS and PhoBR two-component systems (TCSs) deeply feed into the BfmR-mediated regulatory network. In addition, we demonstrated that phoB is required for BfmR to promote the biofilm formation by P. aeruginosa. These results delineate the direct BfmR regulon and exemplify the complexity of BfmR-mediated regulation of cellular functions in P. aeruginosa.

scholarly journals A cassava drought inducible CC-type glutaredoxin, MeGRX232, negatively regulates drought tolerance in Arabidopsis by inhibition of ABA-dependent stomatal closure

2017 ◽  
Author(s):  
Meng-Bin Ruan ◽  
Yi-Ling Yang ◽  
Xin Guo ◽  
Xue Wang ◽  
Bin Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Stomatal Closure ◽  
Ectopic Expression ◽  
Land Plant ◽  
Regulation Of Transcription ◽  
Cassava Leaves ◽  
Genome Wide ◽  
Stress Related Genes

AbstractCC-type glutaredoxins (GRXs) are a land plant-specific GRX subgroup that evolved from CGFS GRXs, and participate in organ development and stress responses through the regulation of transcription factors. Here, genome-wide analysis identified 18 CC-type GRXs in the cassava genome, of which six (MeGRX058, 232, 360, 496, 785, and 892) were induced by drought and ABA stress in cassava leaves. Furthermore, we found that overexpression of MeGRX232 results in drought hypersensitivity in soil-grown plants, with a higher water loss rate, but with increased tolerance of mannitol and ABA in Arabidopsis on the sealed agar plates. The ABA induced stomatal closure is impaired in MeGRX232-OE Arabidopsis. Further analysis reveals that the overexpression of MeGRX232 leads to more ROS accumulation in guard cells. MeGRX232 can interact with TGA5 from Arabidopsis and MeTGA074 from cassava in vitro and in vivo. The results of microarray assays show that MeGRX232-OE affected the expression of a set of drought and oxidative stress related genes. Taken together, we demonstrated that CC-type GRXs involved in ABA signal transduction and play roles in response to drought through regulating stomatal closure.Novelty statement:We found that drought and ABA stress induced the transcription of CC-type glutaredoxins (GRXs) in cassava leaves. Ectopic expression of one of them, MeGRX232 in Arabidopsis affected the sensitivity to abscisic acid (ABA) and mannitol, and caused drought hypersensitivity by impairment of ABA-dependent stomatal closure.

scholarly journals Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanlei Zhai ◽  
Yuanyuan Cui ◽  
Miaoyu Song ◽  
Alexander Vainstein ◽  
Shangwu Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Temperature Response ◽  
Cysteine Proteases ◽  
Ficus Carica ◽  
Protease Gene ◽  
Functional Studies ◽  
Genome Wide ◽  
Genes Encoding ◽  
Localization Analysis

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1–10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207–505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.

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