---
_id: '11344'
abstract:
- lang: eng
  text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
    to be primate-restricted pathogens. The base of their pathogenicity is the type
    3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
    host cell invasion and subsequent proliferation. A large family of T3SS effectors,
    E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
    pathogenicity through the modulation of cellular ubiquitination that degrades
    host proteins. However, recent genomic studies identified ipaH genes in the genomes
    of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
    from fecal samples of bovine calves, suggesting that non-human hosts may also
    be infected by these strains, potentially pathogenic to humans. We performed a
    comparative genomic study of the functional repertoires in the ipaH gene family
    in Shigella and enteroinvasive Escherichia from human and predicted non-human
    hosts. We found that fewer than half of Shigella genomes had a complete set of
    ipaH genes, with frequent gene losses and duplications that were not consistent
    with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
    set of substrate-binding domains and, in contrast to the Shigella proteins, two
    variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
    and composition of effectors indicate horizontal gene transfer between E. coli
    adapted to different hosts. These results provide a framework for understanding
    of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
    study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
  at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
  by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
  and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
  thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
  Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
  der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
  by the European Union’s Horizon 2020 Research and Innovation Programme under the
  Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
  full_name: Dranenko, NO
  last_name: Dranenko
- first_name: MN
  full_name: Tutukina, MN
  last_name: Tutukina
- first_name: MS
  full_name: Gelfand, MS
  last_name: Gelfand
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
citation:
  ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific
    Reports</i>. 2022;12. doi:<a href="https://doi.org/10.1038/s41598-022-10827-3">10.1038/s41598-022-10827-3</a>
  apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva,
    O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
    Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href="https://doi.org/10.1038/s41598-022-10827-3">https://doi.org/10.1038/s41598-022-10827-3</a>
  chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
    “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
    <i>Scientific Reports</i>. Springer Nature, 2022. <a href="https://doi.org/10.1038/s41598-022-10827-3">https://doi.org/10.1038/s41598-022-10827-3</a>.
  ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific
    Reports</i>, vol. 12. Springer Nature, 2022.
  ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
    IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
    Reports. 12, 6868.
  mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
    Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer
    Nature, 2022, doi:<a href="https://doi.org/10.1038/s41598-022-10827-3">10.1038/s41598-022-10827-3</a>.
  short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
    Reports 12 (2022).
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T06:59:49Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
  isi:
  - '000788639400032'
  pmid:
  - '35477739'
file:
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  checksum: 12601b8a5c6b83bb618f92bcb963ecc9
  content_type: application/pdf
  creator: dernst
  date_created: 2022-05-02T09:05:20Z
  date_updated: 2022-05-02T09:05:20Z
  file_id: '11349'
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  file_size: 3564155
  relation: main_file
  success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
  grant_number: I05127
  name: Evolutionary analysis of gene regulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Scientific Reports
publication_identifier:
  issn:
  - 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
  Escherichia
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
  text: Empirical essays of fitness landscapes suggest that they may be rugged, that
    is having multiple fitness peaks. Such fitness landscapes, those that have multiple
    peaks, necessarily have special local structures, called reciprocal sign epistasis
    (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
    quantitative relationship between the number of fitness peaks and the number of
    reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
    et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
    is a necessary but not sufficient condition for the existence of multiple peaks.
    Applying discrete Morse theory, which to our knowledge has never been used in
    this context, we extend this result by giving the minimal number of reciprocal
    sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
  discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
  supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
  (I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
  full_name: Saona Urmeneta, Raimundo J
  id: BD1DF4C4-D767-11E9-B658-BC13E6697425
  last_name: Saona Urmeneta
  orcid: 0000-0001-5103-038X
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
- first_name: Kseniia
  full_name: Khudiakova, Kseniia
  id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
  last_name: Khudiakova
  orcid: 0000-0002-6246-1465
citation:
  ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
    of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin
    of Mathematical Biology</i>. 2022;84(8). doi:<a href="https://doi.org/10.1007/s11538-022-01029-z">10.1007/s11538-022-01029-z</a>
  apa: Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation
    between the number of peaks and the number of reciprocal sign epistatic interactions.
    <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href="https://doi.org/10.1007/s11538-022-01029-z">https://doi.org/10.1007/s11538-022-01029-z</a>
  chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
    “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
    Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022.
    <a href="https://doi.org/10.1007/s11538-022-01029-z">https://doi.org/10.1007/s11538-022-01029-z</a>.
  ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
    the number of peaks and the number of reciprocal sign epistatic interactions,”
    <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.
  ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
    number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
    of Mathematical Biology. 84(8), 74.
  mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
    the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical
    Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href="https://doi.org/10.1007/s11538-022-01029-z">10.1007/s11538-022-01029-z</a>.
  short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
    Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
  isi:
  - '000812509800001'
file:
- access_level: open_access
  checksum: 05a1fe7d10914a00c2bca9b447993a65
  content_type: application/pdf
  creator: dernst
  date_created: 2022-06-20T07:51:32Z
  date_updated: 2022-06-20T07:51:32Z
  file_id: '11455'
  file_name: 2022_BulletinMathBiology_Saona.pdf
  file_size: 463025
  relation: main_file
  success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: '        84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '771209'
  name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
  grant_number: I05127
  name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
  eissn:
  - 1522-9602
  issn:
  - 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
  interactions
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2022'
...