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Article ; Online: Molecular pathway of mitochondrial preprotein import through the TOM-TIM23 supercomplex.

Zhou, Xueyin / Yang, Yuqi / Wang, Guopeng / Wang, Shanshan / Sun, Dongjie / Ou, Xiaomin / Lian, Yuke / Li, Long

2023 Volume 30, Issue 12, Page(s) 1996–2008

Abstract: ... controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane ... The mechanisms through which proteins are translocated via the TOM and TIM23 complexes remain unclear. Here ... we report the assembly of the active TOM-TIM23 supercomplex of Saccharomyces cerevisiae with translocating ...

Abstract	Over half of mitochondrial proteins are imported from the cytosol via the pre-sequence pathway, controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. The mechanisms through which proteins are translocated via the TOM and TIM23 complexes remain unclear. Here we report the assembly of the active TOM-TIM23 supercomplex of Saccharomyces cerevisiae with translocating polypeptide substrates. Electron cryo-microscopy analyses reveal that the polypeptide substrates pass the TOM complex through the center of a Tom40 subunit, interacting with a glutamine-rich region. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17 and Mgr2. The polypeptide substrates are shielded from lipids by Mgr2 and Tim17, which creates a translocation pathway characterized by a negatively charged entrance and a central hydrophobic region. These findings reveal an unexpected pre-sequence pathway through the TOM-TIM23 supercomplex spanning the double membranes of mitochondria.
MeSH term(s)	Membrane Transport Proteins/chemistry ; Mitochondrial Precursor Protein Import Complex Proteins ; Carrier Proteins/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Protein Transport ; Mitochondria/metabolism ; Saccharomyces cerevisiae/metabolism ; Mitochondrial Proteins/metabolism ; Peptides/metabolism ; Membrane Proteins/metabolism
Chemical Substances	Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Carrier Proteins ; Mitochondrial Membrane Transport Proteins ; Saccharomyces cerevisiae Proteins ; Mitochondrial Proteins ; Peptides ; TIM23 protein, S cerevisiae ; Mgr2 protein, S cerevisiae ; Membrane Proteins ; Tom40 protein, S cerevisiae
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-023-01103-7
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Article ; Online: A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors.

Yang, Meijing / Chen, Shuai / Lim, Shey-Li / Yang, Lang / Zhong, Jia Yi / Chan, Koon Chuen / Zhao, Zhizhu / Wong, Kam-Bo / Wang, Junqi / Lim, Boon Leong

Journal of integrative plant biology

2024

Abstract: ... membrane) and the TOM (translocon on the outer mitochondrial membrane) complexes for import ... ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors ...

Abstract	In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon on the outer chloroplast membrane) and the TOM (translocon on the outer mitochondrial membrane) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA
Language	English
Publishing date	2024-03-19
Publishing country	China (Republic : 1949- )
Document type	Journal Article
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13645
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Article: Atomic structure of human TOM core complex.

Wang, Wenhe / Chen, Xudong / Zhang, Laixing / Yi, Jingbo / Ma, Qingxi / Yin, Jian / Zhuo, Wei / Gu, Jinke / Yang, Maojun

Cell discovery

2020 Volume 6, Page(s) 67

Abstract: The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate ... cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins ... The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations ...

Abstract	The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 β-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins.
Language	English
Publishing date	2020-09-29
Publishing country	England
Document type	Journal Article
ISSN	2056-5968
ISSN	2056-5968
DOI	10.1038/s41421-020-00198-2
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Article ; Online: Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors.

Su, Jiayue / Liu, Desheng / Yang, Fan / Zuo, Mei-Qing / Li, Chang / Dong, Meng-Qiu / Sun, Shan / Sui, Sen-Fang

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 26, Page(s) e2200158119

Abstract: ... translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom ... of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function ... as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and ...

Abstract	Mitochondrial preproteins synthesized in cytosol are imported into mitochondria by a multisubunit translocase of the outer membrane (TOM) complex. Functioned as the receptor, the TOM complex components, Tom 20, Tom22, and Tom70, recognize the presequence and further guide the protein translocation. Their deficiency has been linked with neurodegenerative diseases and cardiac pathology. Although several structures of the TOM complex have been reported by cryoelectron microscopy (cryo-EM), how Tom22 and Tom20 function as TOM receptors remains elusive. Here we determined the structure of TOM core complex at 2.53 Å and captured the structure of the TOM complex containing Tom22 and Tom20 cytosolic domains at 3.74 Å. Structural analysis indicates that Tom20 and Tom22 share a similar three-helix bundle structural feature in the cytosolic domain. Further structure-guided biochemical analysis reveals that the Tom22 cytosolic domain is responsible for binding to the presequence, and the helix H1 is critical for this binding. Altogether, our results provide insights into the functional mechanism of the TOM complex recognizing and transferring preproteins across the mitochondrial membrane.
MeSH term(s)	Cryoelectron Microscopy ; Humans ; Mitochondrial Precursor Protein Import Complex Proteins/chemistry ; Protein Domains ; Receptors, Cytoplasmic and Nuclear/chemistry
Chemical Substances	Mitochondrial Precursor Protein Import Complex Proteins ; Receptors, Cytoplasmic and Nuclear ; TOMM20 protein, human ; TOMM22 protein, human
Language	English
Publishing date	2022-06-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2200158119
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Article ; Online: Cross-cultural comparison of theory of mind deficits in patients with schizophrenia from China and Denmark: different aspects of ToM show different results.

Beck, Katrine Ingeman / Simonsen, Arndis / Wang, Huiling / Yang, Liuqing / Zhou, Yuan / Bliksted, Vibeke

Nordic journal of psychiatry

2020 Volume 74, Issue 5, Page(s) 366–373

Abstract: Introduction: ...

Abstract	Introduction:
MeSH term(s)	Adult ; China/ethnology ; Cross-Cultural Comparison ; Denmark/ethnology ; Female ; Humans ; Male ; Middle Aged ; Neuropsychological Tests/standards ; Schizophrenia/diagnosis ; Schizophrenia/ethnology ; Schizophrenic Psychology ; Theory of Mind/physiology ; Young Adult
Language	English
Publishing date	2020-02-10
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	1104974-1
ISSN	1502-4725 ; 0803-9488 ; 0029-1455
ISSN (online)	1502-4725
ISSN	0803-9488 ; 0029-1455
DOI	10.1080/08039488.2020.1723687
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Article ; Online: Streptomyces sp. strain SK68, isolated from peanut rhizosphere, promotes growth and alleviates salt stress in tomato (Solanum lycopersicum cv. Micro-Tom).

Damodharan, Karthiyaini / Palaniyandi, Sasikumar Arunachalam / Le, Bao / Suh, Joo-Won / Yang, Seung Hwan

Journal of microbiology (Seoul, Korea)

2018 Volume 56, Issue 10, Page(s) 753–759

Abstract: ... its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants ...

Abstract	A novel actinobacterium, strain SK68, was isolated from the rhizosphere of peanut plant and its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants. Based on 16S rDNA based phylogenetic analysis, strain SK68 has been identified as a Streptomyces sp. Strain SK68 had branched substrate mycelium bearing smooth surfaced spores and the spore colour is brownish grey on ISP4 medium. It exhibited enzyme activities such as xylanase, cellulase, amylase, and pectinase and degraded hypoxanthine, casein, and L-tyrosine. The strain SK68 differed in its banding pattern in BOX-PCR and RAPD fingerprinting compared to the closely matching type strains Streptomyces erythrochromogenes NBRC 3304
MeSH term(s)	Arachis/microbiology ; Biomass ; DNA, Bacterial/genetics ; Lycopersicon esculentum/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Salinity ; Soil Microbiology ; Streptomyces/classification ; Streptomyces/isolation & purification ; Streptomyces/physiology ; Stress, Physiological
Chemical Substances	DNA, Bacterial ; RNA, Ribosomal, 16S
Language	English
Publishing date	2018-09-28
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2012399-1
ISSN	1976-3794 ; 1225-8873
ISSN (online)	1976-3794
ISSN	1225-8873
DOI	10.1007/s12275-018-8120-5
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Article ; Online: Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato.

Lee, Jinsu / Shim, Donghwan / Moon, Suyun / Kim, Hyemin / Bae, Wonsil / Kim, Kyunghwan / Kim, Yang-Hoon / Rhee, Sung-Keun / Hong, Chang Pyo / Hong, Suk-Young / Lee, Ye-Jin / Sung, Jwakyung / Ryu, Hojin

Plant physiology and biochemistry : PPB

2018 Volume 127, Page(s) 553–560

Abstract: ... Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using ...

Abstract	Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (Solanum lycopersicum), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a SlDWARF gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.
MeSH term(s)	Brassinosteroids/metabolism ; Dehydration/genetics ; Dehydration/metabolism ; Gene Expression Profiling ; Genome-Wide Association Study ; Lycopersicon esculentum/genetics ; Lycopersicon esculentum/metabolism ; Mutation ; Plant Stomata/genetics ; Plant Stomata/metabolism ; Signal Transduction/genetics ; Stress, Physiological/genetics
Chemical Substances	Brassinosteroids
Language	English
Publishing date	2018-04-27
Publishing country	France
Document type	Journal Article
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2018.04.031
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Article ; Online: Streptomyces sp. strain PGPA39 alleviates salt stress and promotes growth of 'Micro Tom' tomato plants.

Palaniyandi, S A / Damodharan, K / Yang, S H / Suh, J W

Journal of applied microbiology

2014 Volume 117, Issue 3, Page(s) 766–773

Abstract: ... stress-alleviating activity of PGPA39 was evaluated using 'Micro Tom' tomato plants with 180 mmol l(-1 ...

Abstract	Aims: To identify an actinobacterial strain that can promote growth and alleviate salinity stress in tomato plants. Methods and results: Actinobacteria were isolated from agricultural soil and screened for ACC deaminase activity, production of indole acetic acid (IAA), solubilization of tricalcium phosphate and sodium chloride (NaCl) salinity tolerance. Among the several strains tested, one strain designated PGPA39 exhibited higher IAA production, and phosphate solubilization in addition to ACC deaminase activity, and tolerance to 1 mol l(-1) NaCl. Strain PGPA39 was identified as a Streptomyces strain based on 16S rDNA sequence and designated Streptomyces sp. strain PGPA39. It promoted the growth of Arabidopsis seedlings in vitro as evidenced by a significant increase in plant biomass and number of lateral roots. Salinity stress-alleviating activity of PGPA39 was evaluated using 'Micro Tom' tomato plants with 180 mmol l(-1) NaCl stress under gnotobiotic condition. A significant increase in plant biomass and chlorophyll content and a reduction in leaf proline content were observed in PGPA39-inoculated tomato plants under salt stress compared with control and salt-stressed noninoculated plants. Conclusions: Streptomyces sp. strain PGPA39 alleviated salt stress and promoted the growth of tomato plants. Significance and impact of the study: This study shows the potential of Streptomyces sp. strain PGPA39 in alleviating salinity stress in tomato plants and could be utilized for stress alleviation in crop plants under field conditions.
MeSH term(s)	Biomass ; Carbon-Carbon Lyases/metabolism ; Indoleacetic Acids/metabolism ; Lycopersicon esculentum/drug effects ; Lycopersicon esculentum/growth & development ; Lycopersicon esculentum/microbiology ; Plant Leaves/microbiology ; Salinity ; Seedlings/growth & development ; Sodium Chloride/pharmacology ; Streptomyces/enzymology ; Streptomyces/isolation & purification ; Streptomyces/metabolism ; Stress, Physiological
Chemical Substances	Indoleacetic Acids ; Sodium Chloride (451W47IQ8X) ; indoleacetic acid (6U1S09C61L) ; 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) ; Carbon-Carbon Lyases (EC 4.1.-)
Language	English
Publishing date	2014-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1358023-1
ISSN	1365-2672 ; 1364-5072
ISSN (online)	1365-2672
ISSN	1364-5072
DOI	10.1111/jam.12563
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Article: Streptomyces sp. strain SK68, isolated from peanut rhizosphere, promotes growth and alleviates salt stress in tomato (Solanum lycopersicum cv. Micro-Tom)

Damodharan, Karthiyaini / Sasikumar Arunachalam Palaniyandi / Bao Le / Joo-Won Suh / Seung Hwan Yang

journal of microbiology. 2018 Oct., v. 56, no. 10

2018

Abstract: ... its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants ...

Abstract	A novel actinobacterium, strain SK68, was isolated from the rhizosphere of peanut plant and its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants. Based on 16S rDNA based phylogenetic analysis, strain SK68 has been identified as a Streptomyces sp. Strain SK68 had branched substrate mycelium bearing smooth surfaced spores and the spore colour is brownish grey on ISP4 medium. It exhibited enzyme activities such as xylanase, cellulase, amylase, and pectinase and degraded hypoxanthine, casein, and L-tyrosine. The strain SK68 differed in its banding pattern in BOX-PCR and RAPD fingerprinting compared to the closely matching type strains Streptomyces erythrochromogenes NBRC 3304ᵀ (AB184746), S. flavotricini NBRC 12770ᵀ (AB184132), S. racemochromogenes NBRC 12906ᵀ (AB184235), and S. polychromogenes NBRC 13072ᵀ (NR041109). Strain SK68 was evaluated for its salinity stress-alleviating activity in tomato plants with 180 mmol/L NaCl under gnotobiotic condition. A significant increase in plant biomass was observed in strain SK68-inoculated tomato plants under salt stress compared to control and salt-stressed non-inoculated plants.
Keywords	Solanum lycopersicum ; Streptomyces flavotricini ; Streptomyces polychromogenes ; Streptomyces racemochromogenes ; amylases ; casein ; color ; endo-1,4-beta-glucanase ; enzyme activity ; hypoxanthine ; mycelium ; peanuts ; phylogeny ; phytomass ; polygalacturonase ; random amplified polymorphic DNA technique ; rhizosphere ; ribosomal DNA ; salinity ; salt stress ; sodium chloride ; spores ; tomatoes ; tyrosine ; xylanases
Language	English
Dates of publication	2018-10
Size	p. 753-759.
Publishing place	The Microbiological Society of Korea
Document type	Article
ZDB-ID	2012399-1
ISSN	1225-8873
ISSN	1225-8873
DOI	10.1007/s12275-018-8120-5
Database	NAL-Catalogue (AGRICOLA)

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Article: Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato

Lee, Jinsu / Bae, Wonsil / Hong, Chang Pyo / Hong, Suk-Young / Kim, Hyemin / Kim, Kyunghwan / Kim, Yang-Hoon / Lee, Ye-Jin / Moon, Suyun / Rhee, Sung-Keun / Ryu, Hojin / Shim, Donghwan / Sung, Jwakyung

Plant physiology and biochemistry. 2018 June, v. 127

2018

Abstract: ... Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using ...

Abstract	Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (Solanum lycopersicum), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a SlDWARF gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.
Keywords	biochemical pathways ; biotic stress ; brassinosteroids ; cell walls ; drought ; drought tolerance ; gene regulatory networks ; genes ; lignification ; models ; mutants ; osmotic stress ; phenotype ; plant growth ; signal transduction ; Solanum lycopersicum ; steroid hormones ; stomatal movement ; stress response ; tomatoes ; transcriptomics ; water stress
Language	English
Dates of publication	2018-06
Size	p. 553-560.
Publishing place	Elsevier Masson SAS
Document type	Article
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2018.04.031
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