Unusual relatives of the multisubunit RNA polymerase

2018 ◽  
Vol 47 (1) ◽  
pp. 219-228 ◽  
Author(s):  
David Forrest
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Kluyveromyces Lactis ◽  
Current Understanding ◽  
Magnesium Binding ◽  
Killer System ◽  
Domains Of Life ◽  
Single Subunit ◽  
Shed Light

AbstractTranscription, the first step of gene expression, is accomplished in all domains of life by the multisubunit RNA polymerase (msRNAP). Accordingly, the msRNAP is an ancient enzyme that is ubiquitous across all cellular organisms. Conserved in absolutely all msRNAPs is the catalytic magnesium-binding aspartate triad and the structural fold it is present on, the double ψ β barrel (DPBB). In-depth bioinformatics has begun to reveal a wealth of unusual proteins distantly related to msRNAP, identified due to their possession of the aspartate triad and DPBB folds. Three examples of these novel RNAPs are YonO of the Bacillus subtilis SPβ prophage, non-virion RNAP (nvRNAP) of the B. subtilis AR9 bacteriophage and ORF6 RNAP of the Kluyveromyces lactis cytoplasmic killer system. While YonO and AR9 nvRNAP are both bacteriophage enzymes, they drastically contrast. YonO is an incredibly minimal single-subunit RNAP, while AR9 nvRNAP is multisubunit bearing much more resemblance to the canonical msRNAP. ORF6 RNAP is an intermediate, given it is a single-subunit enzyme with substantial conservation with the msRNAP. Recent findings have begun to shed light on these polymerases, which have the potential to update our understanding of the mechanisms used for transcription and give new insights into the canonical msRNAP and its evolution. This mini-review serves to introduce and outline our current understanding of these three examples of novel, unusual RNAPs.

scholarly journals Expression of spoIIIJ in the Prespore Is Sufficient for Activation of σG and for Sporulation in Bacillus subtilis

2003 ◽  
Vol 185 (13) ◽  
pp. 3905-3917 ◽  
Author(s):  
Mónica Serrano ◽  
Luísa Côrte ◽  
Jason Opdyke ◽  
Charles P. Moran, ◽  
Adriano O. Henriques
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Sigma Factor ◽  
Vegetative Growth ◽  
Mother Cell ◽  
Asymmetric Division ◽  
Developmental Program ◽  
Inactive Form

ABSTRACT During sporulation in Bacillus subtilis, the prespore-specific developmental program is initiated soon after asymmetric division of the sporangium by the compartment-specific activation of RNA polymerase sigma factor σF. σF directs transcription of spoIIIG, encoding the late forespore-specific regulator σG. Following synthesis, σG is initially kept in an inactive form, presumably because it is bound to the SpoIIAB anti-sigma factor. Activation of σG occurs only after the complete engulfment of the prespore by the mother cell. Mutations in spoIIIJ arrest sporulation soon after conclusion of the engulfment process and prevent activation of σG. Here we show that σG accumulates but is mostly inactive in a spoIIIJ mutant. We also show that expression of the spoIIIGE155K allele, encoding a form of σG that is not efficiently bound by SpoIIAB in vitro, restores σG-directed gene expression to a spoIIIJ mutant. Expression of spoIIIJ occurs during vegetative growth. However, we show that expression of spoIIIJ in the prespore is sufficient for σG activation and for sporulation. Mutations in the mother cell-specific spoIIIA locus are known to arrest sporulation just after completion of the engulfment process. Previous work has also shown that σG accumulates in an inactive form in spoIIIA mutants and that the need for spoIIIA expression for σG activation can be circumvented by the spoIIIGE155K allele. However, in contrast to the case for spoIIIJ, we show that expression of spoIIIA in the prespore does not support efficient sporulation. The results suggest that the activation of σG at the end of the engulfment process involves the action of spoIIIA from the mother cell and of spoIIIJ from the prespore.

scholarly journals One Perturbation of the Mother Cell Gene Regulatory Network Suppresses the Effects of Another during Sporulation of Bacillus subtilis

2007 ◽  
Vol 189 (23) ◽  
pp. 8467-8473 ◽  
Author(s):  
Lijuan Wang ◽  
John Perpich ◽  
Adam Driks ◽  
Lee Kroos
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Regulatory Network ◽  
Mother Cell ◽  
Feedback Loop ◽  
Network Functions ◽  
Regulatory Loop ◽  
Cell Gene ◽  
Spore Coat Protein

ABSTRACT In the mother cell of sporulating Bacillus subtilis, a regulatory network functions to control gene expression. Four transcription factors act sequentially in the order σE, SpoIIID, σK, GerE. σE and σK direct RNA polymerase to transcribe different regulons. SpoIIID and GerE are DNA-binding proteins that activate or repress transcription of many genes. Several negative regulatory loops add complexity to the network. First, transcriptionally active σK RNA polymerase inhibits early sporulation gene expression, resulting in reduced accumulation of σE and SpoIIID late during sporulation. Second, GerE represses sigK transcription, reducing σK accumulation about twofold. Third, SpoIIID represses cotC, which encodes a spore coat protein, delaying its transcription by σK RNA polymerase. Partially circumventing the first feedback loop, by engineering cells to maintain the SpoIIID level late during sporulation, causes spore defects. Here, the effects of circumventing the second feedback loop, by mutating the GerE binding sites in the sigK promoter region, are reported. Accumulation of pro-σK and σK was increased, but no spore defects were detected. Expression of σK-dependent reporter fusions was altered, increasing the expression of gerE-lacZ and cotC-lacZ and decreasing the expression of cotD-lacZ. Because these effects on gene expression were opposite those observed when the SpoIIID level was maintained late during sporulation, cells were engineered to both maintain the SpoIIID level and have elevated sigK expression late during sporulation. This restored the expression of σK-dependent reporters to wild-type levels, and no spore defects were observed. Hence, circumventing the second feedback loop suppressed the effects of perturbing the first feedback loop. By feeding information back into the network, these two loops appear to optimize target gene expression and increase network robustness. Circumventing the third regulatory loop, by engineering cells to express cotC about 2 h earlier than normal, did not cause a detectable spore defect.

scholarly journals Maintaining the Transcription Factor SpoIIID Level Late during Sporulation Causes Spore Defects in Bacillus subtilis

2007 ◽  
Vol 189 (20) ◽  
pp. 7302-7309 ◽  
Author(s):  
Lijuan Wang ◽  
John Perpich ◽  
Adam Driks ◽  
Lee Kroos
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Rna Polymerase ◽  
Mother Cell ◽  
Structural Defects ◽  
Spore Coat ◽  
Multicopy Plasmid ◽  
Altered Expression ◽  
Cell Gene Expression ◽  
Cell Gene

ABSTRACT During sporulation of Bacillus subtilis, four regulatory proteins act in the order σE, SpoIIID, σK, and GerE to temporally control gene expression in the mother cell. σE and σK work sequentially with core RNA polymerase to transcribe different sets of genes. SpoIIID and GerE are small, sequence-specific DNA-binding proteins that activate or repress transcription of many genes. Previous studies showed that transcriptionally active σK RNA polymerase inhibits early mother cell gene expression, reducing accumulation of SpoIIID late in sporulation. Here, the effects of perturbing the mother cell gene regulatory network by maintaining the SpoIIID level late during sporulation are reported. Persistent expression was obtained by fusing spoIIID to the σK-controlled gerE promoter on a multicopy plasmid. Fewer heat- and lysozyme-resistant spores were produced by the strain with persistent spoIIID expression, but the number of spores resistant to organic solvents was unchanged, as was their germination ability. Transmission electron microscopy showed structural defects in the spore coat. Reporter fusions to σK-dependent promoters showed lower expression of gerE and cotC and higher expression of cotD. Altered expression of cot genes, which encode spore coat proteins, may account for the spore structural defects. These results suggest that one role of negative feedback by σK RNA polymerase on early mother cell gene expression is to lower the level of SpoIIID late during sporulation in order to allow normal expression of genes in the σK regulon.

scholarly journals Forespore Signaling Is Necessary for Pro-σK Processing during Bacillus subtilis Sporulation Despite the Loss of SpoIVFA upon Translational Arrest

2002 ◽  
Vol 184 (19) ◽  
pp. 5393-5401 ◽  
Author(s):  
Lee Kroos ◽  
Yuen-Tsu Nicco Yu ◽  
Denise Mills ◽  
Shelagh Ferguson-Miller
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Oxidative Phosphorylation ◽  
Rna Polymerase ◽  
Western Blot ◽  
Blot Analysis ◽  
Mother Cell ◽  
Proteolytic Processing ◽  
Electrochemical Gradient ◽  
Translational Arrest

ABSTRACT The σK checkpoint coordinates gene expression in the mother cell with signaling from the forespore during Bacillus subtilis sporulation. The signaling pathway involves SpoIVB, a serine peptidase produced in the forespore, which is believed to cross the innermost membrane surrounding the forespore and activate a complex of proteins, including BofA, SpoIVFA, and SpoIVFB, located in the outermost membrane surrounding the forespore. Activation of the complex allows proteolytic processing of pro-σK, and the resulting σK RNA polymerase transcribes genes in the mother cell. To investigate activation of the pro-σK processing complex, the level of SpoIVFA in extracts of sporulating cells was examined by Western blot analysis. The SpoIVFA level decreased when pro-σK processing began during sporulation. In extracts of a spoIVB mutant defective in forespore signaling, the SpoIVFA level failed to decrease normally and no processing of pro-σK was observed. Although these results are consistent with a model in which SpoIVFA inhibits processing until the SpoIVB-mediated signal is received from the forespore, we discovered that loss of SpoIVFA was insufficient to allow processing under certain conditions, including static incubation of the culture and continued shaking after the addition of inhibitors of oxidative phosphorylation or translation. Under these conditions, loss of SpoIVFA was independent of spoIVB. The inability to process pro-σK under these conditions was not due to loss of SpoIVFB, the putative processing enzyme, or to a requirement for ongoing synthesis of pro-σK. Rather, it was found that the requirements for shaking of the culture, for oxidative phosphorylation, and for translation could be bypassed by mutations that uncouple processing from dependence on forespore signaling. This suggests that ongoing translation is normally required for efficient pro-σK processing because synthesis of the SpoIVB signal protein is needed to activate the processing complex. When translation is blocked, synthesis of SpoIVB ceases, and the processing complex remains inactive despite the loss of SpoIVFA. Taken together, the results suggest that SpoIVB signaling activates the processing complex by performing another function in addition to causing loss of SpoIVFA or by causing loss of SpoIVFA in a different way than when translation is blocked. The results also demonstrate that the processing machinery can function in the absence of translation or an electrochemical gradient across membranes.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

RNA Polymerase Pauses Precisely and Regulates Gene Expression

2018 ◽  
Author(s):  
Jason A. Watts ◽  
Joshua Burdick ◽  
Jillian Daigneault ◽  
Alan Bruzel ◽  
Zhengwei Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase

scholarly journals CRISPR-assisted multi-dimensional regulation for fine-tuning gene expression in Bacillus subtilis

2019 ◽  
Vol 47 (7) ◽  
pp. e40-e40 ◽  
Author(s):  
Zhenghui Lu ◽  
Shihui Yang ◽  
Xin Yuan ◽  
Yunyun Shi ◽  
Li Ouyang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Fine Tuning
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