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1دورية أكاديمية
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum , a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica , to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica , TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum , activation of ppsA and repression of pykA , is absent in Har. hispanica . Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica . Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
العلاقة: https://figshare.com/articles/journal_contribution/Strains_used_in_this_study_/25008003Test
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s010Test
https://figshare.com/articles/journal_contribution/Strains_used_in_this_study_/25008003Test -
2دورية أكاديمية
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum , a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica , to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica , TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum , activation of ppsA and repression of pykA , is absent in Har. hispanica . Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica . Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
العلاقة: https://figshare.com/articles/journal_contribution/Primers_used_in_this_study_/25008009Test
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s012Test
https://figshare.com/articles/journal_contribution/Primers_used_in_this_study_/25008009Test -
3صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: A) Phylogenetic distribution of TrmB proteins that also contain a carbohydrate-binding domain. B) Multiple sequence alignment of the sugar-binding domain of Har. hispanica TrmB homologs. Red, underlined residues are essential for sugar binding in Tcc. litoralis , conserved residues are in bold underline [ 73 , 74 ]. Asterisks below the alignment denote identical residues and dots represent similar residues. Organism abbreviations and locus tags are as follows: TLI_TRMB, Tcc. litoralis OCC_03542; PFU_TRMBL1, Pyr. furiosus PF0124; TKO_TGR, Tcc. kodakaraensis TK1769; HBT_TRMB, Hbt. salinarum VNG_1451C. Har. hispanica TrmB homologs are named according to their identity to characterized proteins.
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.g002Test
https://figshare.com/articles/figure/Sugar-sensing_TrmB_homologs_/25008018Test -
4صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: A: Summary of variants identified in each strain. “X” indicates that the mutation (rows) was detected in a given strain (columns). Strain designations are given in S1 Table . Representative coverage plots confirming chromosomal deletions for (B) pyrF locus for all strains and (C) trmB Har strains. X-axis provides the genome coordinates. Tables report local read depth, or sequencing coverage, for each strain. D: Confirmation of C-terminal trmB -hemagglutinin fusion used for immunoprecipitation experiments. (TIF)
العلاقة: https://figshare.com/articles/figure/Genotype_confirmation_by_whole-genome_sequencing_/25007976Test
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s001Test
https://figshare.com/articles/figure/Genotype_confirmation_by_whole-genome_sequencing_/25007976Test -
5صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: A: In-trans complementation of Δ trmB Har in both AKS133 and AKS319 backgrounds. Log-transformed, fitted growth curves of complementation strains and strains harboring the empty vector (EV) grown in the presence or absence of glucose. Shaded regions depict the 95% confidence intervals. B: Area under the growth curve (AUC) of (A), with FDR-corrected significance scores. C: Parent strain and Δ trmB Har growth in each condition relative to no carbon, measured by AUC. All growth experiments were done with a minimum of 3 biological replicates, each in technical triplicate. Error bars depict the standard deviation of the mean. (EPS)
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s002Test
https://figshare.com/articles/figure/_i_i_i_trmB_i_growth_/25007979Test -
6صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: A: Fitted, log-transformed growth curves showing that AKS319 phenocopies AKS133, and (B) that there is no significant difference between AKS133 and AKS319 in 25 mM glucose as measured by the area under the curve (AUC). Strain colors are preserved in A and B. ** p -value < 0.01; **** < 0.0001. C: No significant differences in the growth rate of AKS319 cultures prior to RNA extraction between replicates exhibiting pyrF expression and not. Optical density measurements of the cultures harvested for RNA-seq are shown, with corresponding pyrF counts summarized in the table below. D: Average counts per transcript are highly correlated across AKS319 samples regardless of pyrF expression for both -glucose (N = 2) and +glucose conditions (N = 2). Average counts per transcript are highly correlated across AKS319 and AKS133 regardless of pyrF expression for both -glucose (N = 6) and +glucose conditions (N = 8). Average pyrF counts for each comparison are indicated in orange. Data are normalized relative to library size but have not been batch corrected. (TIF)
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s006Test
https://figshare.com/articles/figure/_i_pyrF_i_expression_has_negligible_impact_on_i_i_i_trmB_sub_Har_sub_i_fitness_and_transcriptome_/25007991Test -
7صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Per base coverage of a representative IP sample in the absence of glucose shown in black, an IP sample in glucose is shown in blue. Pile-up was calculated from unextended bam files. The relative location of consensus peaks and motifs is shown below. Magenta bars indicate whether nearby genes were differentially expressed: magenta bars above the line represent genes up-regulated in the Δ trmB Har mutant. The height of the magenta bar represents the magnitude of change, according to the log fold change (LFC) scale bar to the right of each panel. Gene strand orientation and labels are shown in grey. Motif locations are indicated by the vertical blue line within each panel. Numbers above each panel indicate the genomic coordinates and chromosomal element of the region displayed. (EPS)
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s003Test
https://figshare.com/articles/figure/Relative_position_of_genes_consensus_peaks_and_motifs_for_15_regions_identified_by_ChIP-seq_/25007982Test -
8صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Sequences corresponding to peaks were extracted and submitted to XTREME as described in the methods. Yellow highlights indicate the motif reported in Fig 4 . (TIF)
العلاقة: https://figshare.com/articles/figure/Effect_of_background_model_on_discovered_motifs_/25007985Test
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s004Test
https://figshare.com/articles/figure/Effect_of_background_model_on_discovered_motifs_/25007985Test -
9
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Timely regulation of carbon metabolic pathways is essential for cellular processes and to prevent futile cycling of intracellular metabolites. In Halobacterium salinarum , a hypersaline adapted archaeon, a sugar-sensing TrmB family protein controls gluconeogenesis and other biosynthetic pathways. Notably, Hbt. salinarum does not utilize carbohydrates for energy, uncommon among Haloarchaea. We characterized a TrmB-family transcriptional regulator in a saccharolytic generalist, Haloarcula hispanica , to investigate whether the targets and function of TrmB, or its regulon, is conserved in related species with distinct metabolic capabilities. In Har. hispanica , TrmB binds to 15 sites in the genome and induces the expression of genes primarily involved in gluconeogenesis and tryptophan biosynthesis. An important regulatory control point in Hbt. salinarum , activation of ppsA and repression of pykA , is absent in Har. hispanica . Contrary to its role in Hbt. salinarum and saccharolytic hyperthermophiles, TrmB does not act as a global regulator: it does not directly repress the expression of glycolytic enzymes, peripheral pathways such as cofactor biosynthesis, or catabolism of other carbon sources in Har. hispanica . Cumulatively, these findings suggest rewiring of the TrmB regulon alongside metabolic network evolution in Haloarchaea.
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s009Test
https://figshare.com/articles/dataset/Supporting_File_1_/25008000Test -
10صورة
مصطلحات موضوعية: Biochemistry, Medicine, Microbiology, Cell Biology, Genetics, Computational Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, uncommon among haloarchaea, prevent futile cycling, genes primarily involved, findings suggest rewiring, distinct metabolic capabilities, family transcriptional regulator, div >< p, halobacterium salinarum <, haloarcula hispanica <, carbon metabolic pathways, hypersaline adapted archaeon, >, trmb binds, salinarum <, hispanica <, global regulator, carbon sources, adapted archaea, pyka <, ppsa <, peripheral pathways
الوصف: Motif sequences are highlighted in purple. Motif occurrences on opposite strands were considered distinct. Darker purple color indicates motif instances on opposite strands overlap. Start codons are highlighted in grey. Putative initiation elements are bolded and underlined (TATA-box and BRE). Other haloarchaea have been reported to frequently lack identifiable TATA sequences [ 94 ]. If a promoter element could not be identified, the expected location (i.e., -26/-27 for TATA and -33/-34 for BRE) was underlined. (TIF)
الإتاحة: https://doi.org/10.1371/journal.pgen.1011115.s013Test
https://figshare.com/articles/figure/Motif_position_relative_to_predicted_transcription_initiation_elements_for_direct_targets_of_TrmB_sub_Har_sub_/25008012Test
