Two ATP phosphoribosyltransferase isozymes of Geobacter sulfurreducens contribute to growth in the presence or absence of histidine and under nitrogen fixation conditions

2011 ◽  
Vol 57 (7) ◽  
pp. 547-558 ◽  
Author(s):  
Muktak Aklujkar
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Mutational Analysis ◽  
Transcript Abundance ◽  
Geobacter Sulfurreducens ◽  
Growth Defect ◽  
Histidine Biosynthesis ◽  
Growth Defects ◽  
Biosynthesis Gene ◽  
Delayed Growth

Bacteria of the Geobacter clade possess two distinct ATP phosphoribosyltransferases encoded by hisGL and hisGS+hisZ to catalyze the first reaction of histidine biosynthesis. This very unusual redundancy was investigated by mutational analysis. The hisGL, hisGS, and hisZ genes of Geobacter sulfurreducens were deleted, effects on growth and histidine biosynthesis gene expression were evaluated, and deficiencies were complemented with plasmid-borne genes. Both hisGL and hisGS+hisZ encode functional ATP phosphoribosyltransferases. However, deletion of hisGL resulted in no growth defect, whereas deletion of hisGS delayed growth when histidine was not provided. Both deletions increased hisZ transcript abundance, and both ΔhisGS and ΔhisZ mutations increased hisGL transcript abundance. Growth with HisGL alone (due to deletion of either hisGS or hisZ) was better under nitrogen fixation conditions than when ammonium was provided. Deletion of hisZ caused growth defects under all conditions tested, with or without exogenous sources of histidine, with different patterns of histidine biosynthesis gene expression under each condition. Taken together, the data indicate that G. sulfurreducens depends primarily on the HisGSZ isozyme as an ATP phosphoribosyltransferase in histidine biosynthesis, and for other functions when histidine is available; however, HisGL also functions as ATP phosphoribosyltransferase, particularly during nitrogen fixation.

scholarly journals Circadian Rhythm of Nitrogenase Gene Expression in the Diazotrophic Filamentous Nonheterocystous CyanobacteriumTrichodesmium sp. Strain IMS 101

1998 ◽  
Vol 180 (14) ◽  
pp. 3598-3605 ◽  
Author(s):  
Yi-Bu Chen ◽  
Benny Dominic ◽  
Mark T. Mellon ◽  
Jonathan P. Zehr
Keyword(s):  
Gene Expression ◽  
Nitrogen Fixation ◽  
Circadian Rhythm ◽  
Transcription Initiation ◽  
Transcript Abundance ◽  
Endogenous Rhythm ◽  
Filamentous Cyanobacterium ◽  
Nitrogen Fixation Activity ◽  
Fe Protein ◽  
Higher Temperature

ABSTRACT Recent studies suggested that the daily cycle of nitrogen fixation activity in the marine filamentous nonheterocystous cyanobacteriumTrichodesmium sp. is controlled by a circadian rhythm. In this study, we evaluated the rhythm of nitrogen fixation inTrichodesmium sp. strain IMS 101 by using the three criteria for an endogenous rhythm. Nitrogenase transcript abundance oscillated with a period of approximately 24 h, and the cycle was maintained even under constant light conditions. The cyclic pattern of transcript abundance was maintained when the culture was grown at 24 and 28.5°C, although the period was slightly longer (26 h) at the higher temperature. The cycle of gene expression could be entrained with light-dark cues. Results of inhibitor experiments indicated that transcript abundance was regulated primarily by transcription initiation, rather than by degradation. The circadian rhythm, the first conclusively demonstrated endogenous rhythm in a filamentous cyanobacterium, was also reflected in nitrogenase MoFe protein abundance and patterns of Fe protein posttranslational modification-demodification.

scholarly journals Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes

Genetics ◽  
2020 ◽  
Vol 215 (4) ◽  
pp. 1153-1169 ◽  
Author(s):  
Riddhiman K. Garge ◽  
Jon M. Laurent ◽  
Aashiq H. Kachroo ◽  
Edward M. Marcotte
Keyword(s):  
Gene Families ◽  
Growth Defect ◽  
Gene Duplications ◽  
Yeast Gene ◽  
Macromolecular Transport ◽  
Cellular Processes ◽  
Growth Defects ◽  
Yeast Strains ◽  
Human Genes ◽  
Interaction Partners

Many gene families have been expanded by gene duplications along the human lineage, relative to ancestral opisthokonts, but the extent to which the duplicated genes function similarly is understudied. Here, we focused on structural cytoskeletal genes involved in critical cellular processes, including chromosome segregation, macromolecular transport, and cell shape maintenance. To determine functional redundancy and divergence of duplicated human genes, we systematically humanized the yeast actin, myosin, tubulin, and septin genes, testing ∼81% of human cytoskeletal genes across seven gene families for their ability to complement a growth defect induced by inactivation or deletion of the corresponding yeast ortholog. In five of seven families—all but α-tubulin and light myosin, we found at least one human gene capable of complementing loss of the yeast gene. Despite rescuing growth defects, we observed differential abilities of human genes to rescue cell morphology, meiosis, and mating defects. By comparing phenotypes of humanized strains with deletion phenotypes of their interaction partners, we identify instances of human genes in the actin and septin families capable of carrying out essential functions, but failing to fully complement the cytoskeletal roles of their yeast orthologs, thus leading to abnormal cell morphologies. Overall, we show that duplicated human cytoskeletal genes appear to have diverged such that only a few human genes within each family are capable of replacing the essential roles of their yeast orthologs. The resulting yeast strains with humanized cytoskeletal components now provide surrogate platforms to characterize human genes in simplified eukaryotic contexts.

scholarly journals Sight of parasitoid wasps accelerates sexual behavior and upregulates a micropeptide gene in Drosophila

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shimaa A. M. Ebrahim ◽  
Gaëlle J. S. Talross ◽  
John R. Carlson
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Sexual Behavior ◽  
Behavioral Response ◽  
Mutational Analysis ◽  
Parasitoid Wasp ◽  
Parasitoid Wasps ◽  
Wasp Species ◽  
Defensive Responses ◽  
Vast Range

AbstractParasitoid wasps inflict widespread death upon the insect world. Hundreds of thousands of parasitoid wasp species kill a vast range of insect species. Insects have evolved defensive responses to the threat of wasps, some cellular and some behavioral. Here we find an unexpected response of adult Drosophila to the presence of certain parasitoid wasps: accelerated mating behavior. Flies exposed to certain wasp species begin mating more quickly. The effect is mediated via changes in the behavior of the female fly and depends on visual perception. The sight of wasps induces the dramatic upregulation in the fly nervous system of a gene that encodes a 41-amino acid micropeptide. Mutational analysis reveals that the gene is essential to the behavioral response of the fly. Our work provides a foundation for further exploration of how the activation of visual circuits by the sight of a wasp alters both sexual behavior and gene expression.

scholarly journals Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuhua Zhan ◽  
Cortland Griswold ◽  
Lewis Lukens
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Reference Genome ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Rna Seq ◽  
Individual Genome ◽  
Abundance Estimates ◽  
Mapping Bias ◽  
Quantify Gene Expression

Abstract Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species.

Analysis of a tissue-specific enhancer: ARF6 regulates adipogenic gene expression

1992 ◽  
Vol 12 (3) ◽  
pp. 1202-1208
Author(s):  
R A Graves ◽  
P Tontonoz ◽  
B M Spiegelman
Keyword(s):  
Gene Expression ◽  
Cultured Cells ◽  
Mutational Analysis ◽  
Cell Types ◽  
Specific Gene ◽  
Enhancer Activity ◽  
Cis Acting ◽  
Specific Gene Expression ◽  
Nuclear Extracts ◽  
Adipogenic Gene

The molecular basis of adipocyte-specific gene expression is not well understood. We have previously identified a 518-bp enhancer from the adipocyte P2 gene that stimulates adipose-specific gene expression in both cultured cells and transgenic mice. In this analysis of the enhancer, we have defined and characterized a 122-bp DNA fragment that directs differentiation-dependent gene expression in cultured preadipocytes and adipocytes. Several cis-acting elements have been identified and shown by mutational analysis to be important for full enhancer activity. One pair of sequences, ARE2 and ARE4, binds a nuclear factor (ARF2) present in extracts derived from many cell types. Multiple copies of these elements stimulate gene expression from a minimal promoter in preadipocytes, adipocytes, and several other cultured cell lines. A second pair of elements, ARE6 and ARE7, binds a separate factor (ARF6) that is detected only in nuclear extracts derived from adipocytes. The ability of multimers of ARE6 or ARE7 to stimulate promoter activity is strictly adipocyte specific. Mutations in the ARE6 sequence greatly reduce the activity of the 518-bp enhancer. These data demonstrate that several cis- and trans-acting components contribute to the activity of the adipocyte P2 enhancer and suggest that ARF6, a novel differentiation-dependent factor, may be a key regulator of adipogenic gene expression.

The flavin transferase ApbE flavinylates the ferredoxin:NAD+-oxidoreductase Rnf required for N2 fixation in Azotobacter vinelandii

2021 ◽  
Author(s):  
Yulia V Bertsova ◽  
Marina V Serebryakova ◽  
Alexander A Baykov ◽  
Alexander V Bogachev
Keyword(s):  
Nitrogen Fixation ◽  
Azotobacter Vinelandii ◽  
Growth Defect ◽  
Deficient Mutant ◽  
Fixed Nitrogen ◽  
Oxidoreductase Activity ◽  
Threonine Residue ◽  
Ferredoxin Reductase ◽  
Relative Contribution ◽  
Fixation System

Abstract Azotobacter vinelandii, the model microbe in nitrogen fixation studies, uses the ferredoxin:NAD+-oxidoreductase Rnf to regenerate ferredoxin (flavodoxin) acting as an electron donor for nitrogenase. However, the relative contribution of Rnf into nitrogenase functioning is unknown because this bacterium contains another ferredoxin reductase, FixABCX. Furthermore, Rnf is flavinylated in the cell, but the importance and pathway of this modification reaction also remain largely unknown. We have constructed A. vinelandii cells with impaired activities of FixABCX and/or putative flavin transferase ApbE. The ApbE-deficient mutant could not produce covalently flavinylated membrane proteins and demonstrated a markedly decreased flavodoxin:NAD+ oxidoreductase activity and significant growth defect under diazotrophic conditions. The double ΔFix/ΔApbE mutation abolished the flavodoxin:NAD+ oxidoreductase activity and the ability of A. vinelandii to grow in the absence of fixed nitrogen source. ApbE flavinylated a truncated RnfG subunit of Rnf1 by forming a phosphoester bond between FMN and a threonine residue. These findings indicate that Rnf (presumably its Rnf1 form) is the major ferredoxin-reducing enzyme in the nitrogen fixation system and that the activity of Rnf depends on its covalent flavinylation by the flavin transferase ApbE.

Mechanism of RSV-induced IL-8 gene expression in A549 cells before viral replication

1996 ◽  
Vol 271 (6) ◽  
pp. L963-L971 ◽  
Author(s):  
M. A. Fiedler ◽  
K. Wernke-Dollries ◽  
J. M. Stark
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Viral Replication ◽  
Transcriptional Activation ◽  
Mutational Analysis ◽  
A549 Cells ◽  
Nf Kappa B ◽  
Mobility Shift ◽  
Syncytial Virus ◽  
Time Point

Previous studies demonstrated that respiratory syncytial virus (RSV) infection of A549 cells induced interleukin (IL)-8 gene expression and protein release from the cells as early as 2 h after treatment [M. A. Fiedler, K. Wernke-Dollries, and J. M. Stark. Am. J. Physiol. 269 (Lung Cell. Mol. Physiol. 13): L865-L872, 1995; J. G. Mastronarde, M. M. Monick, and G. W. Hunninghake. Am. J. Respir. Cell Mol. Biol. 13: 237-244, 1995]. Furthermore, the effects of RSV at the 2-h time point were not dependent on viral replication. The studies reported here were designed to test the hypothesis that active and inactive RSV induce IL-8 gene expression in A549 cells at the 2-h time point by a mechanism dependent on the activation of the nuclear transcription factor NF-kappa B Northern blot analysis indicated that IL-8 gene expression occurred independent of protein synthesis 2 h after A549 cells were treated with RSV. Analysis of nuclear extracts from RSV-treated A549 cells by electrophoretic mobility shift assays demonstrated that NF-kappa B was activated as early as 15 min after RSV was added to the cells and remained activated for at least 90 min. In contrast, baseline levels of NF-IL-6 and activator protein-1 (AP-1) did not change over this period of time. Deoxyribonuclease footprint analysis of a portion of the 5'-flanking region of the IL-8 gene demonstrated two potential regions for transcription factor binding, which corresponded to the potential AP-1 binding site, and potential NF-IL-6 and NF-kappa B binding sites. Mutational analysis of the 200-bp 5'-untranslated region of the IL-8 gene demonstrated that activation of NF-kappa B and NF-IL-6 were required for RSV-induced transcriptional activation of the IL-8 gene.

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