Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery

  1. Andrea Volante
  2. Juan Carlos Alonso
  3. Kiyoshi Mizuuchi  Is a corresponding author
  1. National Institute of Diabetes and Digestive and Kidney Diseases, United States
  2. National Center for Biotechnology, Spain

Abstract

Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent non-specific DNA binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for all figures presented.

Article and author information

Author details

  1. Andrea Volante

    National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Juan Carlos Alonso

    Department of Microbial Biotechnology, National Center for Biotechnology, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5178-7179
  3. Kiyoshi Mizuuchi

    National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
    For correspondence
    kiyoshimi@niddk.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8193-9244

Funding

National Institute of Diabetes and Digestive and Kidney Diseases

  • Kiyoshi Mizuuchi

Ministerio de Ciencia e Innovación (2018-097054-B-I00,2021AEP031)

  • Juan Carlos Alonso

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jie Xiao, Johns Hopkins University, United States

Version history

  1. Received: April 14, 2022
  2. Preprint posted: May 30, 2022 (view preprint)
  3. Accepted: September 2, 2022
  4. Accepted Manuscript published: September 5, 2022 (version 1)
  5. Version of Record published: September 22, 2022 (version 2)
  6. Version of Record updated: September 23, 2022 (version 3)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 345
    Page views
  • 114
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Andrea Volante
  2. Juan Carlos Alonso
  3. Kiyoshi Mizuuchi
(2022)
Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery
eLife 11:e79480.
https://doi.org/10.7554/eLife.79480

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Riham Ayoubi, Joel Ryan ... Carl Laflamme
    Research Advance

    Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, have demonstrated that: (i) more than 50% of all antibodies failed in one or more applications, (ii) yet, ~50–75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; and (iii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease
    Rui-Qiu Yang, Yong-Hong Chen ... Cheng-Gang Zou
    Research Article

    An imbalance of the gut microbiota, termed dysbiosis, has a substantial impact on host physiology. However, the mechanism by which host deals with gut dysbiosis to maintain fitness remains largely unknown. In Caenorhabditis elegans, Escherichia coli, which is its bacterial diet, proliferates in its intestinal lumen during aging. Here, we demonstrate that progressive intestinal proliferation of E. coli activates the transcription factor DAF-16, which is required for maintenance of longevity and organismal fitness in worms with age. DAF-16 up-regulates two lysozymes lys-7 and lys-8, thus limiting the bacterial accumulation in the gut of worms during aging. During dysbiosis, the levels of indole produced by E. coli are increased in worms. Indole is involved in the activation of DAF-16 by TRPA-1 in neurons of worms. Our finding demonstrates that indole functions as a microbial signal of gut dysbiosis to promote fitness of the host.