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  1. Article: The Underrated Gut Microbiota Helminths, Bacteriophages, Fungi, and Archaea.

    Garcia-Bonete, Maria Jose / Rajan, Anandi / Suriano, Francesco / Layunta, Elena

    Life (Basel, Switzerland)

    2023  Volume 13, Issue 8

    Abstract: The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt ... ...

    Abstract The microbiota inhabits the gastrointestinal tract, providing essential capacities to the host. The microbiota is a crucial factor in intestinal health and regulates intestinal physiology. However, microbiota disturbances, named dysbiosis, can disrupt intestinal homeostasis, leading to the development of diseases. Classically, the microbiota has been referred to as bacteria, though other organisms form this complex group, including viruses, archaea, and eukaryotes such as fungi and protozoa. This review aims to clarify the role of helminths, bacteriophages, fungi, and archaea in intestinal homeostasis and diseases, their interaction with bacteria, and their use as therapeutic targets in intestinal maladies.
    Language English
    Publishing date 2023-08-18
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life13081765
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Global Lrp regulator protein from Haloferax mediterranei: Transcriptional analysis and structural characterization.

    Matarredona, Laura / García-Bonete, María-José / Guío, Jorge / Camacho, Mónica / Fillat, María F / Esclapez, Julia / Bonete, María-José

    International journal of biological macromolecules

    2024  Volume 260, Issue Pt 2, Page(s) 129541

    Abstract: Haloferax mediterranei, an extreme halophilic archaeon thriving in hypersaline environments, has acquired significant attention in biotechnological and biochemical research due to its remarkable ability to flourish in extreme salinity conditions. ... ...

    Abstract Haloferax mediterranei, an extreme halophilic archaeon thriving in hypersaline environments, has acquired significant attention in biotechnological and biochemical research due to its remarkable ability to flourish in extreme salinity conditions. Transcription factors, essential in regulating diverse cellular processes, have become focal points in understanding its adaptability. This study delves into the role of the Lrp transcription factor, exploring its modulation of glnA, nasABC, and lrp gene promoters in vivo through β-galactosidase assays. Remarkably, our findings propose Lrp as the pioneering transcriptional regulator of nitrogen metabolism identified in a haloarchaeon. This study suggests its potential role in activating or repressing assimilatory pathway enzymes (GlnA and NasA). The interaction between Lrp and these promoters is analyzed using Electrophoretic Mobility Shift Assay and Differential Scanning Fluorimetry, highlighting l-glutamine's indispensable role in stabilizing the Lrp-DNA complex. Our research uncovers that halophilic Lrp forms octameric structures in the presence of l-glutamine. The study reveals the three-dimensional structure of the Lrp as a homodimer using X-ray crystallography, confirming this state in solution by Small-Angle X-ray Scattering. These findings illuminate the complex molecular mechanisms driving Hfx. mediterranei's nitrogen metabolism, offering valuable insights about its gene expression regulation and enriching our comprehension of extremophile biology.
    MeSH term(s) Haloferax mediterranei/genetics ; Glutamine/metabolism ; Gene Expression Regulation ; Promoter Regions, Genetic/genetics ; Nitrogen/metabolism
    Chemical Substances Glutamine (0RH81L854J) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2024-01-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.129541
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  3. Article ; Online: The intestinal MUC2 mucin C-terminus is stabilized by an extra disulfide bond in comparison to von Willebrand factor and other gel-forming mucins.

    Gallego, Pablo / Garcia-Bonete, Maria-Jose / Trillo-Muyo, Sergio / Recktenwald, Christian V / Johansson, Malin E V / Hansson, Gunnar C

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1969

    Abstract: The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal domain similar to the MUC5AC and MUC5B mucins and the von ... ...

    Abstract The MUC2 mucin polymer is the main building unit of the intestinal mucus layers separating intestinal microbiota from the host epithelium. The MUC2 mucin is a large glycoprotein with a C-terminal domain similar to the MUC5AC and MUC5B mucins and the von Willebrand factor (VWF). A structural model of the C-terminal part of MUC2, MUC2-C, was generated by combining Cryo-electron microscopy, AlphaFold prediction, information of its glycosylation, and small angle X-ray scattering information. The globular VWD4 assembly in the N-terminal of MUC2-C is followed by 3.5 linear VWC domains that form an extended flexible structure before the C-terminal cystine-knot. All gel-forming mucins and VWF form tail-tail disulfide-bonded dimers in their C-terminal cystine-knot domain, but interestingly the MUC2 mucin has an extra stabilizing disulfide bond on the N-terminal side of the VWD4 domain, likely essential for a stable intestinal mucus barrier.
    MeSH term(s) von Willebrand Factor ; Cystine ; Cryoelectron Microscopy ; Intestines ; Mucin 5AC
    Chemical Substances von Willebrand Factor ; Cystine (48TCX9A1VT) ; Mucin 5AC
    Language English
    Publishing date 2023-04-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37666-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The structure of the second CysD domain of MUC2 and role in mucin organization by transglutaminase-based cross-linking.

    Recktenwald, Christian V / Karlsson, Göran / Garcia-Bonete, Maria-Jose / Katona, Gergely / Jensen, Maja / Lymer, Richard / Bäckström, Malin / Johansson, Malin E V / Hansson, Gunnar C / Trillo-Muyo, Sergio

    Cell reports

    2024  Volume 43, Issue 5, Page(s) 114207

    Abstract: The MUC2 mucin protects the colonic epithelium by a two-layered mucus with an inner attached bacteria-free layer and an outer layer harboring commensal bacteria. CysD domains are 100 amino-acid-long sequences containing 10 cysteines that separate highly ... ...

    Abstract The MUC2 mucin protects the colonic epithelium by a two-layered mucus with an inner attached bacteria-free layer and an outer layer harboring commensal bacteria. CysD domains are 100 amino-acid-long sequences containing 10 cysteines that separate highly O-glycosylated proline, threonine, serine (PTS) regions in mucins. The structure of the second CysD, CysD2, of MUC2 is now solved by nuclear magnetic resonance. CysD2 shows a stable stalk region predicted to be partly covered by adjacent O-glycans attached to neighboring PTS sequences, whereas the CysD2 tip with three flexible loops is suggested to be well exposed. It shows transient dimer interactions at acidic pH, weakened at physiological pH. This transient interaction can be stabilized in vitro and in vivo by transglutaminase 3-catalyzed isopeptide bonds, preferring a specific glutamine residue on one flexible loop. This covalent dimer is modeled suggesting that CysD domains act as connecting hubs for covalent stabilization of mucins to form a protective mucus.
    Language English
    Publishing date 2024-05-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2024.114207
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Bayesian machine learning improves single-wavelength anomalous diffraction phasing.

    Garcia-Bonete, Maria Jose / Katona, Gergely

    Acta crystallographica. Section A, Foundations and advances

    2019  Volume 75, Issue Pt 6, Page(s) 851–860

    Abstract: Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. ... ...

    Abstract Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
    Language English
    Publishing date 2019-10-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2020844-3
    ISSN 2053-2733 ; 1600-5724 ; 0108-7673
    ISSN (online) 2053-2733 ; 1600-5724
    ISSN 0108-7673
    DOI 10.1107/S2053273319011446
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  6. Article ; Online: A practical guide to developing virtual and augmented reality exercises for teaching structural biology.

    Garcia-Bonete, Maria-Jose / Jensen, Maja / Katona, Gergely

    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

    2018  Volume 47, Issue 1, Page(s) 16–24

    Abstract: Although virtual and augmented reality (VR and AR) techniques have been used extensively in specialized laboratories, only recently did they become affordable, reaching wider consumer markets. With increased availability, it is timely to examine the ... ...

    Abstract Although virtual and augmented reality (VR and AR) techniques have been used extensively in specialized laboratories, only recently did they become affordable, reaching wider consumer markets. With increased availability, it is timely to examine the roles that VR and AR may play in teaching structural biology and in experiencing complex data sets such as macromolecular structures. This guide is suitable for those teachers of structural biology who do not have a deep knowledge of information technologies. This study focuses on three questions: 1) How can teachers of structural biology produce and disseminate VR/AR-ready educational material with established and user-friendly software tools?; 2) What are the positive and negative experiences reported by test participants when performing identical learning tasks in the VR and AR environments?; and 3) How do the test participants perceive prerecorded narration during VR/AR exploration? © 2018 International Union of Biochemistry and Molecular Biology, 47(1):16-24, 2018.
    MeSH term(s) Humans ; Molecular Biology/education ; Protein Conformation ; Proteins/chemistry ; Software ; Teaching ; Virtual Reality
    Chemical Substances Proteins
    Language English
    Publishing date 2018-11-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1539-3429
    ISSN (online) 1539-3429
    DOI 10.1002/bmb.21188
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  7. Article: Analysis of Haloferax mediterranei Lrp Transcriptional Regulator

    Matarredona, Laura / Camacho, Mónica / García-Bonete, María-José / Esquerra, Belén / Zafrilla, Basilio / Esclapez, Julia / Bonete, María-José

    Genes. 2021 May 25, v. 12, no. 6

    2021  

    Abstract: Haloferax mediterranei is an extremely halophilic archaeon, able to live in hypersaline environments with versatile nutritional requirements, whose study represents an excellent basis in the field of biotechnology. The transcriptional machinery in ... ...

    Abstract Haloferax mediterranei is an extremely halophilic archaeon, able to live in hypersaline environments with versatile nutritional requirements, whose study represents an excellent basis in the field of biotechnology. The transcriptional machinery in Archaea combines the eukaryotic basal apparatus and the bacterial regulation mechanisms. However, little is known about molecular mechanisms of gene expression regulation compared with Bacteria, particularly in Haloarchaea. The genome of Hfx. mediterranei contains a gene, lrp (HFX_RS01210), which encodes a transcriptional factor belonging to Lrp/AsnC family. It is located downstream of the glutamine synthetase gene (HFX_RS01205), an enzyme involved in ammonium assimilation and amino acid metabolism. To study this transcriptional factor more deeply, the lrp gene has been homologously overexpressed and purified under native conditions by two chromatographic steps, namely nickel affinity and gel filtration chromatography, showing that Lrp behaves asa tetrameric protein of approximately 67 kDa. Its promoter region has been characterized under different growth conditions using bgaH as a reporter gene. The amount of Lrp protein was also analyzed by Western blotting in different nitrogen sources and under various stress conditions. To sum up, regarding its involvement in the nitrogen cycle, it has been shown that its expression profile does not change in response to the nitrogen sources tested. Differences in its expression pattern have been observed under different stress conditions, such as in the presence of hydrogen peroxide or heavy metals. According to these results, the Lrp seems to be involved in a general response against stress factors, acting as a first-line transcriptional regulator.
    Keywords Haloferax mediterranei ; amino acid metabolism ; ammonium ; biotechnology ; gel chromatography ; gene expression regulation ; glutamate-ammonia ligase ; hydrogen peroxide ; hypersalinity ; nickel ; nitrogen ; nitrogen cycle ; promoter regions ; reporter genes ; transcription (genetics) ; transcription factors
    Language English
    Dates of publication 2021-0525
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12060802
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27.

    Jensen, Maja / Chandrasekaran, Venkataragavan / García-Bonete, María-José / Li, Shuxiang / Anindya, Atsarina Larasati / Andersson, Karin / Erlandsson, Malin C / Oparina, Nina Y / Burmann, Björn M / Brath, Ulrika / Panchenko, Anna R / Bokarewa I, Maria / Katona, Gergely

    iScience

    2023  Volume 26, Issue 7, Page(s) 106976

    Abstract: This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We ... ...

    Abstract This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We observed differential expression of PRC2 subunits in CD4
    Language English
    Publishing date 2023-05-29
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.106976
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Analysis of

    Matarredona, Laura / Camacho, Mónica / García-Bonete, María-José / Esquerra, Belén / Zafrilla, Basilio / Esclapez, Julia / Bonete, María-José

    Genes

    2021  Volume 12, Issue 6

    Abstract: Haloferax ... ...

    Abstract Haloferax mediterranei
    MeSH term(s) Amino Acids/metabolism ; Ammonia/metabolism ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Haloferax mediterranei/genetics ; Haloferax mediterranei/metabolism ; Nitrogen/metabolism ; Promoter Regions, Genetic ; Stress, Physiological ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Amino Acids ; Archaeal Proteins ; Transcription Factors ; Ammonia (7664-41-7) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2021-05-25
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12060802
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Estimating the difference between structure-factor amplitudes using multivariate Bayesian inference.

    Katona, Gergely / Garcia-Bonete, Maria José / Lundholm, Ida V

    Acta crystallographica. Section A, Foundations and advances

    2016  Volume 72, Issue Pt 3, Page(s) 406–411

    Abstract: In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the ... ...

    Abstract In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for improving the estimate, the data analysis should also maximally exploit the covariance between the measurements. In X-ray crystallography the difference between structure-factor amplitudes carries important information to solve experimental phasing problems or to determine time-dependent structural changes in pump-probe experiments. Here a multivariate Bayesian method was used to analyse intensity measurement pairs to determine their underlying structure-factor amplitudes and their differences. The posterior distribution of the model parameter was approximated with a Markov chain Monte Carlo algorithm. The described merging method is shown to be especially advantageous when systematic and random errors result in recording negative intensity measurements.
    Language English
    Publishing date 2016--01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020844-3
    ISSN 2053-2733 ; 1600-5724 ; 0108-7673
    ISSN (online) 2053-2733 ; 1600-5724
    ISSN 0108-7673
    DOI 10.1107/S2053273316003430
    Database MEDical Literature Analysis and Retrieval System OnLINE

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