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Article ; Online: Molecular condensation and mechanoregulation of plant class I formin, an integrin‐like actin nucleator

Ma, Zhiming / Zhu, Kexin / Gao, Yong‐Gui / Tan, Suet‐Mien / Miao, Yansong

The FEBS Journal. 2023 July, v. 290, no. 13 p.3336-3354

2023

Abstract: The actin cytoskeleton (AC) undergoes rapid remodelling to coordinate cellular processes during signal transduction, including changes in actin nucleation, crosslinking, and depolymerization in a time‐ and space‐dependent manner. Switching the initial ... ...

Abstract	The actin cytoskeleton (AC) undergoes rapid remodelling to coordinate cellular processes during signal transduction, including changes in actin nucleation, crosslinking, and depolymerization in a time‐ and space‐dependent manner. Switching the initial actin nucleation often provides timely control of the entire actin network formation. Located at the cell surface, the plant class I formin family is a major class of actin nucleators that rapidly respond to exterior chemical and environmental cues. Plant class I formins are structurally integrated within the plant cell wall‐plasma membrane‐actin cytoskeleton (CW‐PM‐AC) continuum, sharing similar biophysical properties to mammalian integrins that are embedded within the extracellular matrix‐PM‐AC continuum. In plants, perturbation of structural components of the CW‐PM‐AC continuum changes the biophysical properties of two dimensional‐scaffolding structures, which results in uncontrolled molecular diffusion and interactions of class I formins, as well as their clustering and activities in the nucleation of the AC. Emerging studies have shown that the PM‐integrated formins are highly responsive to the mechanical perturbation of CW and AC integrity changes that tune the oligomerization and condensation of formin on the cell surface. However, during diverse signalling transductions, the molecular mechanisms that spatiotemporally underlie the mechanosensing and mechanoregulation of formin for remodelling actin remain unclear. Here, the emphasis will be placed on recent developments in understanding how the molecular condensation of class I formin regulates the biochemical activities in tuning actin polymerization during plant immune signalling, as well as how the plant structural components of the CW‐PM‐AC continuum control formin condensation at a nanometre scale.
Keywords	actin ; crosslinking ; depolymerization ; integrins ; mammals ; microfilaments ; oligomerization ; polymerization ; signal transduction
Language	English
Dates of publication	2023-07
Size	p. 3336-3354.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16571
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Article ; Online: Quantitative Proteomics of Medium-Sized Extracellular Vesicle-Enriched Plasma of Lacunar Infarction for the Discovery of Prognostic Biomarkers.

Datta, Arnab / Chen, Christopher / Gao, Yong-Gui / Sze, Siu Kwan

International journal of molecular sciences

2022 Volume 23, Issue 19

Abstract: Lacunar infarction (LACI), a subtype of acute ischemic stroke, has poor mid- to long-term prognosis due to recurrent vascular events or incident dementia which is difficult to predict using existing clinical data. Herein, we aim to discover blood-based ... ...

Abstract	Lacunar infarction (LACI), a subtype of acute ischemic stroke, has poor mid- to long-term prognosis due to recurrent vascular events or incident dementia which is difficult to predict using existing clinical data. Herein, we aim to discover blood-based biomarkers for LACI as a complementary prognostic tool. Convalescent plasma was collected from forty-five patients following a non-disabling LACI along with seventeen matched control subjects. The patients were followed up prospectively for up to five years to record an occurrence of adverse outcome and grouped accordingly (i.e., LACI-no adverse outcome, LACI-recurrent vascular event, and LACI-cognitive decline without any recurrence of vascular events). Medium-sized extracellular vesicles (MEVs), isolated from the pooled plasma of four groups, were analyzed by stable isotope labeling and 2D-LC-MS/MS. Out of 573 (FDR < 1%) quantified proteins, 146 showed significant changes in at least one LACI group when compared to matched healthy control. A systems analysis revealed that major elements (~85%) of the MEV proteome are different from the proteome of small-sized extracellular vesicles obtained from the same pooled plasma. The altered MEV proteins in LACI patients are mostly reduced in abundance. The majority of the shortlisted MEV proteins are not linked to commonly studied biological processes such as coagulation, fibrinolysis, or inflammation. Instead, they are linked to oxygen-glucose deprivation, endo-lysosomal trafficking, glucose transport, and iron homeostasis. The dataset is provided as a web-based data resource to facilitate meta-analysis, data integration, and targeted large-scale validation.
MeSH term(s)	Biomarkers/metabolism ; Chromatography, Liquid ; Extracellular Vesicles/metabolism ; Glucose ; Humans ; Iron ; Ischemic Stroke ; Oxygen ; Prognosis ; Proteome/metabolism ; Proteomics ; Stroke, Lacunar ; Tandem Mass Spectrometry
Chemical Substances	Biomarkers ; Proteome ; Iron (E1UOL152H7) ; Glucose (IY9XDZ35W2) ; Oxygen (S88TT14065)
Language	English
Publishing date	2022-10-01
Publishing country	Switzerland
Document type	Journal Article ; Meta-Analysis
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms231911670
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Article ; Online: Ribosome Protection Proteins-"New" Players in the Global Arms Race with Antibiotic-Resistant Pathogens.

Ero, Rya / Yan, Xin-Fu / Gao, Yong-Gui

International journal of molecular sciences

2021 Volume 22, Issue 10

Abstract: Bacteria have evolved an array of mechanisms enabling them to resist the inhibitory effect of antibiotics, a significant proportion of which target the ribosome. Indeed, resistance mechanisms have been identified for nearly every antibiotic that is ... ...

Abstract	Bacteria have evolved an array of mechanisms enabling them to resist the inhibitory effect of antibiotics, a significant proportion of which target the ribosome. Indeed, resistance mechanisms have been identified for nearly every antibiotic that is currently used in clinical practice. With the ever-increasing list of multi-drug-resistant pathogens and very few novel antibiotics in the pharmaceutical pipeline, treatable infections are likely to become life-threatening once again. Most of the prevalent resistance mechanisms are well understood and their clinical significance is recognized. In contrast, ribosome protection protein-mediated resistance has flown under the radar for a long time and has been considered a minor factor in the clinical setting. Not until the recent discovery of the ATP-binding cassette family F protein-mediated resistance in an extensive list of human pathogens has the significance of ribosome protection proteins been truly appreciated. Understanding the underlying resistance mechanism has the potential to guide the development of novel therapeutic approaches to evade or overcome the resistance. In this review, we discuss the latest developments regarding ribosome protection proteins focusing on the current antimicrobial arsenal and pharmaceutical pipeline as well as potential implications for the future of fighting bacterial infections in the time of "superbugs."
MeSH term(s)	ATP-Binding Cassette Transporters/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacterial Infections/drug therapy ; Bacterial Proteins/metabolism ; Drug Resistance, Bacterial/drug effects ; Drug Resistance, Microbial/physiology ; Drug Resistance, Multiple/drug effects ; Models, Molecular ; Protein Biosynthesis/drug effects ; Ribosomal Proteins/drug effects ; Ribosomal Proteins/metabolism ; Ribosomes/drug effects ; Ribosomes/metabolism
Chemical Substances	ATP-Binding Cassette Transporters ; Anti-Bacterial Agents ; Bacterial Proteins ; Ribosomal Proteins
Language	English
Publishing date	2021-05-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22105356
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Article: Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum‐sensing system in Burkholderia cenocepacia

Yan, Xin‐Fu / Yang, Chunxi / Wang, Mingfang / Yong, Yonlada / Deng, Yinyue / Gao, Yong‐Gui

FEBS letters. 2022 Jan., v. 596, no. 1

2022

Abstract: Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum‐sensing signaling molecule cis‐2‐dodecenoic acid (BDSF). As a bacterial enhancer‐binding protein (bEBP), GtrR is composed of an N‐terminal receiver domain, a ...

Abstract	Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum‐sensing signaling molecule cis‐2‐dodecenoic acid (BDSF). As a bacterial enhancer‐binding protein (bEBP), GtrR is composed of an N‐terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ⁵⁴‐interaction domain, and a C‐terminal helix‐turn‐helix DNA‐binding domain. In this work, we solved its AAA+ ATPase domain in both apo and GTP‐bound forms. The structure revealed how GtrR specifically recognizes GTP. In addition, we also revealed that GtrR has moderate GTPase activity in vitro in the absence of its activation signal. Finally, we found the residues K170, D236, R311, and R357 in GtrR that are crucial to its biological function, any single mutation leading to completely abolishing GtrR activity.
Keywords	Burkholderia cenocepacia ; DNA-binding domains ; adenosinetriphosphatase ; guanosinetriphosphatase ; mutation ; quorum sensing ; transcription factors
Language	English
Dates of publication	2022-01
Size	p. 71-80.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14244
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Article ; Online: Emerging evidence for kindlin oligomerization and its role in regulating kindlin function.

Bu, Wenting / Levitskaya, Zarina / Tan, Suet-Mien / Gao, Yong-Gui

Journal of cell science

2021 Volume 134, Issue 8

Abstract: Integrin-mediated cell-extracellular matrix (ECM) interactions play crucial roles in a broad range of physiological and pathological processes. Kindlins are important positive regulators of integrin activation. The FERM-domain-containing kindlin family ... ...

Abstract	Integrin-mediated cell-extracellular matrix (ECM) interactions play crucial roles in a broad range of physiological and pathological processes. Kindlins are important positive regulators of integrin activation. The FERM-domain-containing kindlin family comprises three members, kindlin-1, kindlin-2 and kindlin-3 (also known as FERMT1, FERMT2 and FERMT3), which share high sequence similarity (identity >50%), as well as domain organization, but exhibit diverse tissue-specific expression patterns and cellular functions. Given the significance of kindlins, analysis of their atomic structures has been an attractive field for decades. Recently, the structures of kindlin and its β-integrin-bound form have been obtained, which greatly advance our understanding of the molecular functions that involve kindlins. In particular, emerging evidence indicates that oligomerization of kindlins might affect their integrin binding and focal adhesion localization, positively or negatively. In this Review, we presented an update on the recent progress of obtaining kindlin structures, and discuss the implication for integrin activation based on kindlin oligomerization, as well as the possible regulation of this process.
Language	English
Publishing date	2021-04-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.256115
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Article ; Online: Molecular condensation and mechanoregulation of plant class I formin, an integrin-like actin nucleator.

Ma, Zhiming / Zhu, Kexin / Gao, Yong-Gui / Tan, Suet-Mien / Miao, Yansong

The FEBS journal

2022 Volume 290, Issue 13, Page(s) 3336–3354

Abstract: The actin cytoskeleton (AC) undergoes rapid remodelling to coordinate cellular processes during signal transduction, including changes in actin nucleation, crosslinking, and depolymerization in a time- and space-dependent manner. Switching the initial ... ...

Abstract	The actin cytoskeleton (AC) undergoes rapid remodelling to coordinate cellular processes during signal transduction, including changes in actin nucleation, crosslinking, and depolymerization in a time- and space-dependent manner. Switching the initial actin nucleation often provides timely control of the entire actin network formation. Located at the cell surface, the plant class I formin family is a major class of actin nucleators that rapidly respond to exterior chemical and environmental cues. Plant class I formins are structurally integrated within the plant cell wall-plasma membrane-actin cytoskeleton (CW-PM-AC) continuum, sharing similar biophysical properties to mammalian integrins that are embedded within the extracellular matrix-PM-AC continuum. In plants, perturbation of structural components of the CW-PM-AC continuum changes the biophysical properties of two dimensional-scaffolding structures, which results in uncontrolled molecular diffusion and interactions of class I formins, as well as their clustering and activities in the nucleation of the AC. Emerging studies have shown that the PM-integrated formins are highly responsive to the mechanical perturbation of CW and AC integrity changes that tune the oligomerization and condensation of formin on the cell surface. However, during diverse signalling transductions, the molecular mechanisms that spatiotemporally underlie the mechanosensing and mechanoregulation of formin for remodelling actin remain unclear. Here, the emphasis will be placed on recent developments in understanding how the molecular condensation of class I formin regulates the biochemical activities in tuning actin polymerization during plant immune signalling, as well as how the plant structural components of the CW-PM-AC continuum control formin condensation at a nanometre scale.
MeSH term(s)	Animals ; Actins/metabolism ; Formins/metabolism ; Microfilament Proteins/metabolism ; Integrins/metabolism ; Actin Cytoskeleton/metabolism ; Plants/metabolism ; Mammals/metabolism
Chemical Substances	Actins ; Formins ; Microfilament Proteins ; Integrins
Language	English
Publishing date	2022-07-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16571
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Article ; Online: Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum-sensing system in Burkholderia cenocepacia.

Yan, Xin-Fu / Yang, Chunxi / Wang, Mingfang / Yong, Yonlada / Deng, Yinyue / Gao, Yong-Gui

FEBS letters

2021 Volume 596, Issue 1, Page(s) 71–80

Abstract: Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum-sensing signaling molecule cis-2-dodecenoic acid (BDSF). As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a ...

Abstract	Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum-sensing signaling molecule cis-2-dodecenoic acid (BDSF). As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ
MeSH term(s)	Burkholderia cenocepacia
Language	English
Publishing date	2021-12-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.14244
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Article ; Online: Cryo-EM structure of the entire FtsH-HflKC AAA protease complex.

Qiao, Zhu / Yokoyama, Tatsuhiko / Yan, Xin-Fu / Beh, Ing Tsyr / Shi, Jian / Basak, Sandip / Akiyama, Yoshinori / Gao, Yong-Gui

Cell reports

2022 Volume 39, Issue 9, Page(s) 110890

Abstract: The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC ...

Abstract	The membrane-bound AAA protease FtsH is the key player controlling protein quality in bacteria. Two single-pass membrane proteins, HflK and HflC, interact with FtsH to modulate its proteolytic activity. Here, we present structure of the entire FtsH-HflKC complex, comprising 12 copies of both HflK and HflC, all of which interact reciprocally to form a cage, as well as four FtsH hexamers with periplasmic domains and transmembrane helices enclosed inside the cage and cytoplasmic domains situated at the base of the cage. FtsH K61/D62/S63 in the β2-β3 loop in the periplasmic domain directly interact with HflK, contributing to complex formation. Pull-down and in vivo enzymatic activity assays validate the importance of the interacting interface for FtsH-HflKC complex formation. Structural comparison with the substrate-bound human m-AAA protease AFG3L2 offers implications for the HflKC cage in modulating substrate access to FtsH. Together, our findings provide a better understanding of FtsH-type AAA protease holoenzyme assembly and regulation.
MeSH term(s)	ATP-Dependent Proteases/metabolism ; ATPases Associated with Diverse Cellular Activities/metabolism ; Bacterial Proteins/metabolism ; Cryoelectron Microscopy ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Humans
Chemical Substances	Bacterial Proteins ; Escherichia coli Proteins ; ATP-Dependent Proteases (EC 3.4.21.-) ; FtsH protein, E coli (EC 3.4.21.-) ; AFG3L2 protein, human (EC 3.4.24.-) ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-)
Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.110890
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Article ; Online: Ribosome protection by ABC-F proteins-Molecular mechanism and potential drug design.

Ero, Rya / Kumar, Veerendra / Su, Weixin / Gao, Yong-Gui

Protein science : a publication of the Protein Society

2019 Volume 28, Issue 4, Page(s) 684–693

Abstract: Members of the ATP-binding cassette F (ABC-F) proteins confer resistance to several classes of clinically important antibiotics through ribosome protection. Recent structures of two ABC-F proteins, Pseudomonas aeruginosa MsrE and Bacillus subtilis VmlR ... ...

Abstract	Members of the ATP-binding cassette F (ABC-F) proteins confer resistance to several classes of clinically important antibiotics through ribosome protection. Recent structures of two ABC-F proteins, Pseudomonas aeruginosa MsrE and Bacillus subtilis VmlR bound to ribosome have shed light onto the ribosome protection mechanism whereby drug resistance is mediated by the antibiotic resistance domain (ARD) connecting the two ATP binding domains. ARD of the E site bound MsrE and VmlR extends toward the drug binding region within the peptidyl transferase center (PTC) and leads to conformational changes in the P site tRNA acceptor stem, the PTC, and the drug binding site causing the release of corresponding drugs. The structural similarities and differences of the MsrE and VmlR structures likely highlight an universal ribosome protection mechanism employed by antibiotic resistance (ARE) ABC-F proteins. The variable ARD domains enable this family of proteins to adapt the protection mechanism for several classes of ribosome-targeting drugs. ARE ABC-F genes have been found in numerous pathogen genomes and multi-drug resistance conferring plasmids. Collectively they mediate resistance to a broader range of antimicrobial agents than any other group of resistance proteins and play a major role in clinically significant drug resistance in pathogenic bacteria. Here, we review the recent structural and biochemical findings on these emerging resistance proteins, offering an update of the molecular basis and implications for overcoming ABC-F conferred drug resistance.
MeSH term(s)	ATP-Binding Cassette Transporters/chemistry ; ATP-Binding Cassette Transporters/metabolism ; Animals ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacteria/metabolism ; Bacterial Infections/drug therapy ; Bacterial Infections/microbiology ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Drug Design ; Drug Resistance, Bacterial ; Humans ; Models, Molecular
Chemical Substances	ATP-Binding Cassette Transporters ; Anti-Bacterial Agents ; Bacterial Proteins
Language	English
Publishing date	2019-03-04
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3589
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Structural and biochemical characterization of novel carbonic anhydrases from Phaeodactylum tricornutum.

Jin, Shengyang / Vullo, Daniela / Bua, Silvia / Nocentini, Alessio / Supuran, Claudiu T / Gao, Yong Gui

Acta crystallographica. Section D, Structural biology

2020 Volume 76, Issue Pt 7, Page(s) 676–686

Abstract: Carbonic anhydrases (CAs) are a well characterized family of metalloenzymes that are highly efficient in facilitating the interconversion between carbon dioxide and bicarbonate. Recently, CA activity has been associated with the LCIB (limiting ... ...

Abstract	Carbonic anhydrases (CAs) are a well characterized family of metalloenzymes that are highly efficient in facilitating the interconversion between carbon dioxide and bicarbonate. Recently, CA activity has been associated with the LCIB (limiting CO
MeSH term(s)	Carbon Dioxide/metabolism ; Carbonic Anhydrases/chemistry ; Diatoms/enzymology ; Photosynthesis ; Protein Structure, Tertiary
Chemical Substances	Carbon Dioxide (142M471B3J) ; Carbonic Anhydrases (EC 4.2.1.1)
Language	English
Publishing date	2020-06-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798320007202
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