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Article ; Online: Structure of mitotic chromosomes.

Beel, Andrew J / Azubel, Maia / Matteï, Pierre-Jean / Kornberg, Roger D

2021 Volume 81, Issue 21, Page(s) 4369–4376.e3

Abstract: Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because ...

Abstract	Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers.
MeSH term(s)	Amino Acid Motifs ; Chromatin/chemistry ; Chromosomes/ultrastructure ; Cryoelectron Microscopy ; DNA/chemistry ; Green Fluorescent Proteins/metabolism ; HeLa Cells ; Histones/chemistry ; Humans ; Microscopy, Fluorescence ; Mitosis ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Spermidine/chemistry ; Tomography
Chemical Substances	Chromatin ; Histones ; Nucleosomes ; Green Fluorescent Proteins (147336-22-9) ; DNA (9007-49-2) ; Spermidine (U87FK77H25)
Language	English
Publishing date	2021-09-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.08.020
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Article: Structure of mitotic chromosomes

Beel, Andrew J. / Azubel, Maia / Matteï, Pierre-Jean / Kornberg, Roger D.

Molecular cell. 2021 Nov. 04, v. 81, no. 21

2021

Abstract	Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers.
Keywords	DNA ; chromosome morphology ; mitosis ; nucleosomes ; tomography
Language	English
Dates of publication	2021-1104
Size	p. 4369-4376.e3.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2021.08.020
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Article ; Online: Bridging cell wall biosynthesis and bacterial morphogenesis.

Matteï, Pierre-Jean / Neves, David / Dessen, Andréa

Current opinion in structural biology

2010 Volume 20, Issue 6, Page(s) 749–755

Abstract: The bacterial cell wall is a complex three-dimensional structure that protects the cell from environmental stress and ensures its shape. The biosynthesis of its main component, the peptidoglycan, involves the coordination of activities of proteins ... ...

Abstract	The bacterial cell wall is a complex three-dimensional structure that protects the cell from environmental stress and ensures its shape. The biosynthesis of its main component, the peptidoglycan, involves the coordination of activities of proteins present in the cytoplasm, the membrane, and the periplasm, some of which also interact with the bacterial cytoskeleton. The sheer complexity of the cell wall elongation process, which is the main focus of this review, has created a significant challenge for the study of the macromolecular interactions that regulate peptidoglycan biosynthesis. The availability of new structural and biochemical data on a number of components of peptidoglycan assembly machineries, including a complex between MreB and RodZ as well as structures of penicillin-binding proteins (PBPs) from a number of pathogenic species, now provide novel insight into the underpinnings of an intricate molecular machinery.
MeSH term(s)	Bacteria/cytology ; Bacteria/growth & development ; Bacteria/metabolism ; Bacterial Proteins/metabolism ; Cell Membrane/chemistry ; Cell Membrane/metabolism ; Cell Wall/metabolism ; Cytoplasm/metabolism ; Morphogenesis
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2010-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2010.09.014
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Article ; Online: Ultra-high field magnetic resonance imaging of the quadriceps tendon enthesis in healthy subjects.

Guenoun, Daphne / Wirth, Theo / Roche, Damien / Michel, Constance P / Daudé, Pierre / Ogier, Augustin C / Chagnaud, Christophe / Mattei, Jean Pierre / Pini, Lauriane / Guye, Maxime / Ollivier, Matthieu / Bendahan, David / Guis, Sandrine

Surgical and radiologic anatomy : SRA

2023 Volume 45, Issue 8, Page(s) 1049–1054

Abstract: Purpose: Although enthesitis is a hallmark of several rheumatologic conditions, current imaging methods are still unable to characterize entheses changes because of the corresponding short transverse relaxation times (T2). A growing number of MR studies ...

Abstract	Purpose: Although enthesitis is a hallmark of several rheumatologic conditions, current imaging methods are still unable to characterize entheses changes because of the corresponding short transverse relaxation times (T2). A growing number of MR studies have used Ultra-High Field (UHF) MRI in order to assess low-T2 tissues e.g., tendon but never in humans. The purpose of the present study was to assess in vivo the enthesis of the quadriceps tendon in healthy subjects using UHF MRI. Methods: Eleven healthy subjects volunteered in an osteoarthritis imaging study. The inclusion criteria were: no knee trauma, Lequesne index = 0, less than 3 h of sport activities per week, and Kellgren and Lawrence grade = 0. 3D MR images were acquired at 7 T using GRE sequences and a T2* mapping. Regions of interest i.e., trabecular bone, subchondral bone, enthesis, and tendon body were identified, and T2* values were quantified and compared. Results: Quadriceps tendon enthesis was visible as a hyper-intense signal. The largest and the lowest T2* values were quantified in the subchondral bone region and the tendon body respectively. T2* value within subchondral bone was significantly higher than T2* value within the enthesis. T2* in subchondral bone region was significantly higher than the whole tendon body T2. Conclusion:* A T2* gradient was observed along the axis from the enthesis toward the tendon body. It illustrates different water biophysical properties. These results provide normative values which could be used in the field of inflammatory rheumatologic diseases and mechanical disorders affecting the tendon.
MeSH term(s)	Humans ; Healthy Volunteers ; Tendons/diagnostic imaging ; Imaging, Three-Dimensional/methods ; Magnetic Resonance Imaging/methods ; Arthritis, Rheumatoid
Language	English
Publishing date	2023-06-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	632839-8
ISSN	1279-8517 ; 0930-312X ; 0930-1038
ISSN (online)	1279-8517
ISSN	0930-312X ; 0930-1038
DOI	10.1007/s00276-023-03175-y
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Article: Improved Metastatic-Free Survival after Systematic Re-Excision Following Complete Macroscopic Unplanned Excision of Limb or Trunk Soft Tissue Sarcoma.

Gouin, Francois / Michot, Audrey / Jafari, Mehrdad / Honoré, Charles / Mattei, Jean Camille / Rochwerger, Alexandre / Ropars, Mickael / Tzanis, Dimitri / Anract, Philippe / Carrere, Sébastien / Gangloff, Dimitri / Ducoulombier, Agnès / Lebbe, Céleste / Guiramand, Jérôme / Waast, Denis / Marchal, Frédéric / Sirveaux, François / Causeret, Sylvain / Gimbergues, Pierre /

Fiorenza, Fabrice / Paquette, Brice / Soibinet, Pauline / Guilloit, Jean-Marc / Le Nail, Louis R / Dujardin, Franck / Brinkert, David / Chemin-Airiau, Claire / Morelle, Magali / Meeus, Pierre / Karanian, Marie / Le Loarer, François / Vaz, Gualter / Blay, Jean-Yves

Cancers

2024 Volume 16, Issue 7

Abstract: Background: Whether re-excision (RE) of a soft tissue sarcoma (STS) of limb or trunk should be systematized as adjuvant care and if it would improve metastatic free survival (MFS) are still debated. The impact of resection margins after unplanned ... ...

Abstract	Background: Whether re-excision (RE) of a soft tissue sarcoma (STS) of limb or trunk should be systematized as adjuvant care and if it would improve metastatic free survival (MFS) are still debated. The impact of resection margins after unplanned macroscopically complete excision (UE) performed out of a NETSARC reference center or after second resection was further investigated. Methods: This large nationwide series used data from patients having experienced UE outside of a reference center from 2010 to 2019, collected in a French nationwide exhaustive prospective cohort NETSARC. Patient characteristics and survival distributions in patients reexcised (RE) or not (No-RE) are reported. Multivariate Cox proportional hazard model was conducted to adjust for classical prognosis factors. Subgroup analysis were performed to identify which patients may benefit from RE. Results: Out of 2371 patients with UE for STS performed outside NETSARC reference centers, 1692 patients were not reviewed by multidisciplinary board before treatment decision and had a second operation documented. Among them, 913 patients experienced re-excision, and 779 were not re-excised. Characteristics were significantly different regarding patient age, tumor site, size, depth, grade and histotype in patients re-excised (RE) or not (No-RE). In univariate analysis, final R0 margins are associated with a better MFS, patients with R1 margins documented at first surgery had a better MFS as compared to patients with first R0 resection. The study identified RE as an independent favorable factor for MFS (HR 0.7, 95% CI 0.53-0.93; Conclusions: RE might be considered in patients with STS of limb or trunk, with UE with macroscopic complete resection performed out of a reference center, and also in originally defined R0 margin resections, to improve LRFS and MFS. Systematic RE should not be advocated for patients older than 70 years, or with tumors greater than 10 cm.
Language	English
Publishing date	2024-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers16071365
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Article ; Online: Uncoupling Promoter Opening from Start-Site Scanning.

Murakami, Kenji / Mattei, Pierre-Jean / Davis, Ralph E / Jin, Huiyan / Kaplan, Craig D / Kornberg, Roger D

Molecular cell

2015 Volume 59, Issue 1, Page(s) 133–138

Abstract: Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so ...

Abstract	Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so Pol II is presumed to "scan" further downstream before starting transcription in yeast. Here we report that removal of the kinase complex TFIIK from TFIIH shifts the TSS in a yeast system upstream to the location observed in metazoans. Conversely, moving the normal TSS to an upstream location enables a high level of TFIIK-independent transcription in the yeast system. We distinguish two stages of the transcription initiation process: bubble formation by TFIIH, which fills the Pol II active center with single-stranded DNA, and subsequent scanning downstream, also driven by TFIIH, which requires displacement of the initial bubble. Omission of TFIIK uncouples the two stages of the process.
MeSH term(s)	Base Sequence ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; RNA Polymerase II/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factor TFIIH/genetics ; Transcription Factor TFIIH/metabolism ; Transcription Initiation Site/physiology ; Transcription, Genetic/genetics
Chemical Substances	Saccharomyces cerevisiae Proteins ; Transcription Factor TFIIH (148710-81-0) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2015-07-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2015.05.021
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Article ; Online: Molecular architecture of the PBP2–MreC core bacterial cell wall synthesis complex

Carlos Contreras-Martel / Alexandre Martins / Chantal Ecobichon / Daniel Maragno Trindade / Pierre-Jean Matteï / Samia Hicham / Pierre Hardouin / Meriem El Ghachi / Ivo G. Boneca / Andréa Dessen

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 10

Abstract: Bacterial wall biosynthesis is a complex process that requires the coordination of multiple enzymes. Here, the authors structurally characterize the PBP2:MreC complex involved in peptidoglycan elongation and cross-linking, and demonstrate that its ... ...

Abstract	Bacterial wall biosynthesis is a complex process that requires the coordination of multiple enzymes. Here, the authors structurally characterize the PBP2:MreC complex involved in peptidoglycan elongation and cross-linking, and demonstrate that its disruption leads to loss of H. pylori shape and inability to sustain growth.
Keywords	Science ; Q
Language	English
Publishing date	2017-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular architecture of the PBP2–MreC core bacterial cell wall synthesis complex

Carlos Contreras-Martel / Alexandre Martins / Chantal Ecobichon / Daniel Maragno Trindade / Pierre-Jean Matteï / Samia Hicham / Pierre Hardouin / Meriem El Ghachi / Ivo G. Boneca / Andréa Dessen

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 10

Abstract	Bacterial wall biosynthesis is a complex process that requires the coordination of multiple enzymes. Here, the authors structurally characterize the PBP2:MreC complex involved in peptidoglycan elongation and cross-linking, and demonstrate that its disruption leads to loss of H. pylori shape and inability to sustain growth.
Keywords	Science ; Q
Language	English
Publishing date	2017-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular architecture of the PBP2-MreC core bacterial cell wall synthesis complex.

Contreras-Martel, Carlos / Martins, Alexandre / Ecobichon, Chantal / Trindade, Daniel Maragno / Matteï, Pierre-Jean / Hicham, Samia / Hardouin, Pierre / Ghachi, Meriem El / Boneca, Ivo G / Dessen, Andréa

Nature communications

2017 Volume 8, Issue 1, Page(s) 776

Abstract: Bacterial cell wall biosynthesis is an essential process that requires the coordinated activity of peptidoglycan biosynthesis enzymes within multi-protein complexes involved in cell division (the "divisome") and lateral wall growth (the "elongasome"). ... ...

Abstract	Bacterial cell wall biosynthesis is an essential process that requires the coordinated activity of peptidoglycan biosynthesis enzymes within multi-protein complexes involved in cell division (the "divisome") and lateral wall growth (the "elongasome"). MreC is a structural protein that serves as a platform during wall elongation, scaffolding other essential peptidoglycan biosynthesis macromolecules, such as penicillin-binding proteins. Despite the importance of these multi-partite complexes, details of their architecture have remained elusive due to the transitory nature of their interactions. Here, we present the crystal structures of the soluble PBP2:MreC core elongasome complex from Helicobacter pylori, and of uncomplexed PBP2. PBP2 recognizes the two-winged MreC molecule upon opening of its N-terminal region, revealing a hydrophobic zipper that serves as binding platform. The PBP2:MreC interface is essential both for protein recognition in vitro and maintenance of bacterial shape and growth. This work allows visualization as to how peptidoglycan machinery proteins are scaffolded, revealing interaction regions that could be targeted by tailored inhibitors.Bacterial wall biosynthesis is a complex process that requires the coordination of multiple enzymes. Here, the authors structurally characterize the PBP2:MreC complex involved in peptidoglycan elongation and cross-linking, and demonstrate that its disruption leads to loss of H. pylori shape and inability to sustain growth.
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Binding Sites ; Cell Wall/metabolism ; Crystallography, X-Ray ; Helicobacter pylori/genetics ; Helicobacter pylori/metabolism ; Models, Molecular ; Penicillin-Binding Proteins/chemistry ; Penicillin-Binding Proteins/genetics ; Protein Structure, Tertiary ; Sequence Alignment
Chemical Substances	Bacterial Proteins ; MreC protein, Bacteria ; Penicillin-Binding Proteins
Language	English
Publishing date	2017-10-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-017-00783-2
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Article ; Online: Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson, Philip J / Trnka, Michael J / Bushnell, David A / Davis, Ralph E / Mattei, Pierre-Jean / Burlingame, Alma L / Kornberg, Roger D

Cell

2016 Volume 166, Issue 6, Page(s) 1411–1422.e16

Abstract: A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure ... ...

Abstract	A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.
MeSH term(s)	Cryoelectron Microscopy ; Gene Expression Regulation ; Mass Spectrometry ; Mediator Complex/chemistry ; Mediator Complex/metabolism ; Models, Molecular ; Phosphorylation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; RNA Polymerase II/chemistry ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Mediator Complex ; Protein Subunits ; Saccharomyces cerevisiae Proteins ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2016-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.08.050
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