scholarly journals Origins and Molecular Evolution of the NusG Paralog RfaH

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Bing Wang ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Igor B. Zhulin ◽  
Irina Artsimovitch
Keyword(s):  
Transcription Factors ◽  
Molecular Evolution ◽  
Rna Polymerase ◽  
Housekeeping Genes ◽  
Content Type ◽  
Bacterial Phyla ◽  
Evolutionary Origins ◽  
Genes Encoding ◽  
Domains Of Life ◽  
Polymerase Binding

ABSTRACT The only universally conserved family of transcription factors comprises housekeeping regulators and their specialized paralogs, represented by well-studied NusG and RfaH. Despite their ubiquity, little information is available on the evolutionary origins, functions, and gene targets of the NusG family members. We built a hidden Markov model profile of RfaH and identified its homologs in sequenced genomes. While NusG is widespread among bacterial phyla and coresides with genes encoding RNA polymerase and ribosome in all except extremely reduced genomes, RfaH is mostly limited to Proteobacteria and lacks common gene neighbors. RfaH activates only a few xenogeneic operons that are otherwise silenced by NusG and Rho. Phylogenetic reconstructions reveal extensive duplications and horizontal transfer of rfaH genes, including those borne by plasmids, and the molecular evolution pathway of RfaH, from “early” exclusion of the Rho terminator and tightened RNA polymerase binding to “late” interactions with the ops DNA element and autoinhibition, which together define the RfaH regulon. Remarkably, NusG is not only ubiquitous in Bacteria but also common in plants, where it likely modulates the transcription of plastid genes. IMPORTANCE In all domains of life, NusG-like proteins make contacts similar to those of RNA polymerase and promote pause-free transcription yet may play different roles, defined by their divergent interactions with nucleic acids and accessory proteins, in the same cell. This duality is illustrated by Escherichia coli NusG and RfaH, which silence and activate xenogenes, respectively. We combined sequence analysis and recent functional and structural insights to envision the evolutionary transformation of NusG, a core regulator that we show is present in all cells using bacterial RNA polymerase, into a virulence factor, RfaH. Our results suggest a stepwise conversion of a NusG duplicate copy into a sequence-specific regulator which excludes NusG from its targets but does not compromise the regulation of housekeeping genes. We find that gene duplication and lateral transfer give rise to a surprising diversity within the only ubiquitous family of transcription factors.

scholarly journals Ancient Transcription Factors in the News

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Irina Artsimovitch ◽  
Stefan H. Knauer
Keyword(s):  
Transcription Factors ◽  
Nucleic Acids ◽  
Rna Polymerase ◽  
Rna Processing ◽  
Binding Sites ◽  
Rna Synthesis ◽  
Mechanistic Studies ◽  
Elongation Complex ◽  
Content Type ◽  
Domains Of Life

ABSTRACTIn every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. InEscherichiacoli, NusG stimulates silencing of horizontally acquired genes, while its paralog RfaH counters NusG action by activating a subset of these genes. Acting alone or as part of regulatory complexes, NusG factors can promote uninterrupted RNA synthesis, bring about transcription pausing or premature termination, modulate RNA processing, and facilitate translation. Recent structural and mechanistic studies of NusG homologs from all domains of life reveal molecular details of multifaceted interactions that underpin their unexpectedly diverse regulatory roles. NusG proteins share conserved binding sites on RNA polymerase and many effects on the transcription elongation complex but differ in their mechanisms of recruitment, interactions with nucleic acids and secondary partners, and regulatory outcomes. Strikingly, some can alternate between autoinhibited and activated states that possess dramatically different secondary structures to achieve exquisite target specificity.

scholarly journals Genetic and Functional Investigation of Zn 2 Cys 6 Transcription Factors RSE2 and RSE3 in Podospora anserina

2013 ◽  
Vol 13 (1) ◽  
pp. 53-65 ◽  
Author(s):  
Elodie Bovier ◽  
Carole H. Sellem ◽  
Adeline Humbert ◽  
Annie Sainsard-Chanet
Keyword(s):  
Transcription Factors ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Constitutive Expression ◽  
Podospora Anserina ◽  
Loss Of Function ◽  
Gene Encoding ◽  
Content Type ◽  
Zinc Cluster ◽  
Wide Range ◽  
Genes Encoding

ABSTRACT In Podospora anserina , the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase ( aox ) when the mitochondrial electron transport chain is impaired. In parallel, they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase ( pck ) and fructose-1,6-biphosphatase ( fbp ). Orthologues of these transcription factors are present in a wide range of filamentous fungi, and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organization of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of the aox gene. We identified 10 independent mutations in 9 positions in rse2 and 11 mutations in 5 positions in rse3 . Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-terminal activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations in rse2 or rse3 . It showed that in addition to aox , fbp , and pck , RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn 2 Cys 6 transcription factor, a flavohemoglobin, and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both an rse2 gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids, and α-ketoglutarate pools.

scholarly journals Direct Target Network of the Neurospora crassa Plant Cell Wall Deconstruction Regulators CLR-1, CLR-2, and XLR-1

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
James P. Craig ◽  
Samuel T. Coradetti ◽  
Trevor L. Starr ◽  
N. Louise Glass
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Transcription Factors ◽  
Neurospora Crassa ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Nutrient Sensing ◽  
Wall Material ◽  
Content Type ◽  
Genes Encoding

ABSTRACTFungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. InNeurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. WhenN. crassais exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog inSaccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex.IMPORTANCEUnderstanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

scholarly journals Determination of RNA polymerase binding surfaces of transcription factors by NMR spectroscopy

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Johanna Drögemüller ◽  
Martin Strauß ◽  
Kristian Schweimer ◽  
Marcel Jurk ◽  
Paul Rösch ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nmr Spectroscopy ◽  
Rna Polymerase ◽  
Polymerase Binding

scholarly journals Regulation of Chlamydia Gene Expression by Tandem Promoters with Different Temporal Patterns

2015 ◽  
Vol 198 (2) ◽  
pp. 363-369 ◽  
Author(s):  
Christopher J. Rosario ◽  
Ming Tan
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Expression Patterns ◽  
Dna Supercoiling ◽  
Early Gene ◽  
Developmental Cycle ◽  
Content Type ◽  
Intracellular Infection

ABSTRACTChlamydiais a genus of pathogenic bacteria with an unusual intracellular developmental cycle marked by temporal waves of gene expression. The three main temporal groups of chlamydial genes are proposed to be controlled by separate mechanisms of transcriptional regulation. However, we have noted genes with discrepancies, such as the early genednaKand the midcycle genesbioYandpgk, which have promoters controlled by the late transcriptional regulators EUO and σ28. To resolve this issue, we analyzed the promoters of these three genesin vitroand inChlamydia trachomatisbacteria grown in cell culture. Transcripts from the σ28-dependent promoter of each gene were detected only at late times in the intracellular infection, bolstering the role of σ28RNA polymerase in late gene expression. In each case, however, expression prior to late times was due to a second promoter that was transcribed by σ66RNA polymerase, which is the major form of chlamydial polymerase. These results demonstrate that chlamydial genes can be transcribed from tandem promoters with different temporal profiles, leading to a composite expression pattern that differs from the expression profile of a single promoter. In addition, tandem promoters allow a gene to be regulated by multiple mechanisms of transcriptional regulation, such as DNA supercoiling or late regulation by EUO and σ28. We discuss how tandem promoters broaden the repertoire of temporal gene expression patterns in the chlamydial developmental cycle and can be used to fine-tune the expression of specific genes.IMPORTANCEChlamydiais a pathogenic bacterium that is responsible for the majority of infectious disease cases reported to the CDC each year. It causes an intracellular infection that is characterized by coordinated expression of chlamydial genes in temporal waves. Chlamydial transcription has been shown to be regulated by DNA supercoiling, alternative forms of RNA polymerase, and transcription factors, but the number of transcription factors found inChlamydiais far fewer than the number found in most bacteria. This report describes the use of tandem promoters that allow the temporal expression of a gene or operon to be controlled by more than one regulatory mechanism. This combinatorial strategy expands the range of expression patterns that are available to regulate chlamydial genes.

scholarly journals Rapid adaptation often occurs through mutations to the most highly conserved positions of the RNA polymerase core enzyme

2021 ◽  
Author(s):  
Yasmin Cohen ◽  
Ruth Hershberg
Keyword(s):  
Rna Polymerase ◽  
Active Site ◽  
Housekeeping Genes ◽  
Pleiotropic Effects ◽  
Apparent Discrepancy ◽  
Rapid Adaptation ◽  
Selective Pressures ◽  
Bacterial Phylogeny ◽  
Core Enzyme ◽  
Genes Encoding

Mutations to the genes encoding the RNA polymerase core enzyme (RNAPC) and additional housekeeping regulatory genes were found to be involved in rapid adaptation, in the context of numerous evolutionary experiments, in which bacteria were exposed to diverse selective pressures. This provides a conundrum, as the housekeeping genes that were so often mutated in response to these diverse selective pressures tend to be among the genes that are most conserved in their sequences across the bacterial phylogeny. In order to further examine this apparent discrepancy, we characterized the precise positions of the RNAPC involved in adaptation to a large variety of selective pressures. We found that different positions of the RNAPC are involved in adaptation to various stresses, with very little overlap found between stresses. We further found that RNAPC positions involved in adaptation tended to be more evolutionary conserved, were more likely to occur within defined protein domains, and tended to be closer to the complex's active site, compared to all other RNAPC positions. Finally, we could show that this observed trend of higher conservation of positions involved in rapid adaptation extends beyond the RNAPC to additional housekeeping genes. Combined, our results demonstrate that the positions that change most readily in response to well defined selective pressures exerted in lab environments are also those that evolve most slowly in nature. This suggests that such adaptations may not readily occur in nature, due to their antagonistically pleiotropic effects, or that if they do occur in nature, they are highly transient.

scholarly journals Mutations in the β-Subunit of the RNA Polymerase Impair the Surface-Associated Motility and Virulence of Acinetobacter baumannii

2017 ◽  
Vol 85 (8) ◽  
Author(s):  
María Pérez-Varela ◽  
Jordi Corral ◽  
Juan Andrés Vallejo ◽  
Soraya Rumbo-Feal ◽  
Germán Bou ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Acinetobacter Baumannii ◽  
Point Mutations ◽  
Β Subunit ◽  
Gene Encoding ◽  
Antibiotic Resistant ◽  
Content Type ◽  
Knockout Mutants ◽  
Genes Encoding ◽  
Spontaneous Mutants

ABSTRACT Acinetobacter baumannii is a major cause of antibiotic-resistant nosocomial infections worldwide. In this study, several rifampin-resistant spontaneous mutants obtained from the A. baumannii ATCC 17978 strain that differed in their point mutations in the rpoB gene, encoding the β-subunit of the RNA polymerase, were isolated. All the mutants harboring amino acid substitutions in position 522 or 540 of the RpoB protein were impaired in surface-associated motility and had attenuated virulence in the fertility model of Caenorhabditis elegans. The transcriptional profile of these mutants included six downregulated genes encoding proteins homologous to transporters and metabolic enzymes widespread among A. baumannii clinical isolates. The construction of knockout mutants in each of the six downregulated genes revealed a significant reduction in the surface-associated motility and virulence of four of them in the A. baumannii ATCC 17978 strain, as well as in the virulent clinical isolate MAR002. Taken together, our results provide strong evidence of the connection between motility and virulence in this multiresistant nosocomial pathogen.

Mechanisms of action of RNA polymerase-binding transcription factors that do not bind to DNA

BIOPHYSICS ◽  
2009 ◽  
Vol 54 (5) ◽  
pp. 555-568 ◽  
Author(s):  
E. V. Stepanova ◽  
A. B. Shevelev ◽  
S. I. Borukhov ◽  
K. V. Severinov
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase ◽  
Mechanisms Of Action ◽  
Polymerase Binding

Molecular mechanisms of archaeal RNA polymerase

2009 ◽  
Vol 37 (1) ◽  
pp. 12-17 ◽  
Author(s):  
Dina Grohmann ◽  
Angela Hirtreiter ◽  
Finn Werner
Keyword(s):  
Transcription Factors ◽  
Nucleic Acid ◽  
Rna Polymerase ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Rna Polymerases ◽  
Nucleic Acid Binding ◽  
Regulatory Interactions ◽  
Cellular Life ◽  
Domains Of Life

All cellular life depends on multisubunit RNAPs (RNA polymerases) that are evolutionarily related through the three domains of life. Archaeal RNAPs encompass 12 subunits that contribute in different ways to the assembly and stability of the enzyme, nucleic acid binding, catalysis and specific regulatory interactions with transcription factors. The recent development of methods to reconstitute archaeal RNAP from recombinant materials in conjunction with structural information of multisubunit RNAPs present a potent opportunity to investigate the molecular mechanisms of transcription.

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