SmiA is a hybrid priming/scaffolding adaptor for the LonA protease in Bacillus subtilis

Olney, Stephen G.; Kearns, Daniel B.

doi:10.1016/j.jbc.2022.102045

Cited by 6 publications

(5 citation statements)

References 54 publications

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“…The FlhDC master flagellar regulator of E. coli/S.enterica is also bipartite, and while the literature disagrees on which protein(s) binds DNA, productive flagellar gene transcription only occurs in the presence of both (7,(84)(85)(86)(87)(88). Finally, SwrA, RcsA, Sxy, and FlhC all regulate either long operons or transmembrane nanomachines and each is proteolytically regulated by the Lon protease (17,(89)(90)(91)(92). Perhaps complex enzymes or machines encoded in long operons require UP elements and consequentially evolved heteromeric transcription factors to activate gene expression in response to environmental input.…”

Section: Discussionmentioning

confidence: 99%

SwrA extends DegU over an UP element to activate flagellar gene expression inBacillus subtilis

Mishra¹,

Hughes²,

Amon³

et al. 2023

Preprint

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SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes.

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Section: Discussionmentioning

confidence: 99%

SwrA extends DegU over an UP element to activate flagellar gene expression inBacillus subtilis

Mishra¹,

Hughes²,

Amon³

et al. 2023

Preprint

Self Cite

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“…It degrades protein substrates in a processive fashion (Li, Hsieh, et al, 2021 ). As stated previously, it uses SmiA as an adaptator for SwrA degradation (Hughes et al, 2018 ; Olney et al, 2022 ). Unexpectedly, PrkA, which for a long time has been wrongly annotated as a protein kinase, is able to hydrolyze an exogenous substrate of Lon proteases, alpha‐casein, in an ATP‐dependent manner.…”

Section: The Proteostasis Networkmentioning

confidence: 99%

“…The swrAA gene appears to result from a recent horizontal gene transfer or de novo creation. When intact, stoichiometric excess of SmiA causes substrate‐independent inhibition of LonA‐dependent turnover (Olney et al, 2022 ).…”

Section: Collective Behaviour Of Bacillus Subtilis ...mentioning

confidence: 99%

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Bremer

Calteau

Danchin

et al. 2023

Microbial Biotechnology

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The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).

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“…While allosteric activators, and at least one substrate-specific adaptor protein, have been identified for bacterial Lon protease, to our knowledge there are no such reports for human LONP1. [51][52][53][54][55] In the absence of adaptor proteins, the NTD must fulfill key regulatory functions regarding substrate recognition and processing. Recently published structures of LONP1 by two groups have defined the complex, interconnected assembly of the NTD that is suggestive of hardwired allosteric regulation in LONP1 (Figure 1).…”

Section: Ntd-mediated Allostery In Lonp1 Functionmentioning

confidence: 99%

Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism

Mindrebo,

Lander

2024

Preprint

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AAA+ enzymes use energy from ATP hydrolysis to remodel diverse cellular targets. Structures of substrate-bound AAA+ complexes suggest that these enzymes employ a conserved hand-over-hand mechanism to thread substrates through their central pore. However, the fundamental aspects of the mechanisms governing motor function and substrate processing within specific AAA+ families remain unresolved. We used cryo-electron microscopy to structurally interrogate reaction intermediates from in vitro biochemical assays to inform the underlying regulatory mechanisms of the human mitochondrial AAA+ protease, LONP1. Our results demonstrate that substrate binding allosterically regulates proteolytic activity, and that LONP1 can adopt a configuration conducive to substrate translocation even when the ATPases are bound to ADP. These results challenge the conventional understanding of the hand-over-hand translocation mechanism, giving rise to an alternative model that aligns more closely with biochemical and biophysical data on related enzymes like ClpX, ClpA, the 26S proteasome, and Lon protease.

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SmiA is a hybrid priming/scaffolding adaptor for the LonA protease in Bacillus subtilis

Cited by 6 publications

References 54 publications

SwrA extends DegU over an UP element to activate flagellar gene expression inBacillus subtilis

SwrA extends DegU over an UP element to activate flagellar gene expression inBacillus subtilis

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism

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