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Hu J, Wang J, Muhammad T, Tuerdiyusufu D, Yang T, Li N, Yang H, Wang B, Yu Q. Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108589. [PMID: 38593485 DOI: 10.1016/j.plaphy.2024.108589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Carotenoids are important pigmented nutrients synthesized by tomato fruits during ripening. To reveal the molecular mechanism underlying carotenoid synthesis during tomato fruit ripening, we analyzed carotenoid metabolites and transcriptomes in six development stages of tomato fruits. A total of thirty different carotenoids were detected and quantified in tomato fruits from 10 to 60 DPA. Based on differential gene expression profiles and WGCNA, we explored several genes that were highly significant and negatively correlated with lycopene, all of which encode fasciclin-like arabinogalactan proteins (FLAs). The FLAs are involved in plant signal transduction, however the functional role of these proteins has not been studied in tomato. Genome-wide analysis revealed that cultivated and wild tomato species contained 18 to 22 FLA family members, clustered into four groups, and mainly evolved by means of segmental duplication. The functional characterization of FLAs showed that silencing of SlFLA1, 5, and 13 were found to contribute to the early coloration of tomato fruits, and the expression of carotenoid synthesis-related genes was up-regulated in fruits that changed phenotypically, especially in SlFLA13-silenced plants. Furthermore, the content of multiple carotenoids (including (E/Z)-phytoene, lycopene, γ-carotene, and α-carotene) was significantly increased in SlFLA13-silenced fruits, suggesting that SlFLA13 has a potential inhibitory function in regulating carotenoid synthesis in tomato fruits. The results of the present study broaden the idea of analyzing the biological functions of tomato FLAs and preliminary evidence for the inhibitory role of SlFLA13 in carotenoid synthesis in fruit, providing the theoretical basis and a candidate for improving tomato fruit quality.
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Affiliation(s)
- Jiahui Hu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Tayeb Muhammad
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Diliaremu Tuerdiyusufu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Mitermite M, Elizari JMU, Ma R, Farrell D, Gordon SV. Exploring virulence in Mycobacterium bovis: clues from comparative genomics and perspectives for the future. Ir Vet J 2023; 76:26. [PMID: 37770951 PMCID: PMC10540498 DOI: 10.1186/s13620-023-00257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Here we provide a summary of a plenary lecture delivered on Mycobacterium bovis, the bovine TB bacillus, at the M. bovis 2022 meeting held in Galway, Ireland, in June 2022. We focus on the analysis of genetic differences between M. bovis and the human pathogen Mycobacterium tuberculosis as a route to gain knowledge on what makes M. bovis function as an animal pathogen. We provide a brief historical background around M. bovis and comparative virulence experiments with M. tuberculosis, before moving to what we have learned from the studies of the M. bovis genome sequence. We discuss the need to translate knowledge on the molecular basis of virulence in M. bovis into improved control of bovine tuberculosis.
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Affiliation(s)
- Morgane Mitermite
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Jose Maria Urtasun Elizari
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
- UCD Conway Institute, University College Dublin, Dublin, Ireland.
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Zvi-Kedem T, Vintila S, Kleiner M, Tchernov D, Rubin-Blum M. Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels. ISME COMMUNICATIONS 2023; 3:48. [PMID: 37210404 PMCID: PMC10199937 DOI: 10.1038/s43705-023-00254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 04/25/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
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Affiliation(s)
- Tal Zvi-Kedem
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 3498838, Israel
| | - Maxim Rubin-Blum
- Biology Department, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, 3108000, Israel.
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4
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Kornilov FD, Slonimskiy YB, Lunegova DA, Egorkin NA, Savitskaya AG, Kleymenov SY, Maksimov EG, Goncharuk SA, Mineev KS, Sluchanko NN. Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP. Commun Biol 2023; 6:471. [PMID: 37117801 PMCID: PMC10147662 DOI: 10.1038/s42003-023-04832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023] Open
Abstract
Fasciclins (FAS1) are ancient adhesion protein domains with no common small ligand binding reported. A unique microalgal FAS1-containing astaxanthin (AXT)-binding protein (AstaP) binds a broad repertoire of carotenoids by a largely unknown mechanism. Here, we explain the ligand promiscuity of AstaP-orange1 (AstaPo1) by determining its NMR structure in complex with AXT and validating this structure by SAXS, calorimetry, optical spectroscopy and mutagenesis. α1-α2 helices of the AstaPo1 FAS1 domain embrace the carotenoid polyene like a jaw, forming a hydrophobic tunnel, too short to cap the AXT β-ionone rings and dictate specificity. AXT-contacting AstaPo1 residues exhibit different conservation in AstaPs with the tentative carotenoid-binding function and in FAS1 proteins generally, which supports the idea of AstaP neofunctionalization within green algae. Intriguingly, a cyanobacterial homolog with a similar domain structure cannot bind carotenoids under identical conditions. These structure-activity relationships provide the first step towards the sequence-based prediction of the carotenoid-binding FAS1 members.
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Affiliation(s)
- Fedor D Kornilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Daria A Lunegova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Anna G Savitskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
| | - Sergey Yu Kleymenov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Street, 119334, Moscow, Russia
| | - Eugene G Maksimov
- M.V. Lomonosov Moscow State University, Faculty of Biology, 119991, Moscow, Russia
| | - Sergey A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, Moscow, Russia.
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
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Gao Y, Yang H, Li L, Gao X, Li M, Dong J, Zhang M, Zhang J, Li X, Lu Z, Burford MA. Higher resistance of a microcystin (MC)-producing cyanobacterium, Microcystis, to the submerged macrophyte Myriophyllum spicatum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:63941-63952. [PMID: 37055695 DOI: 10.1007/s11356-023-26654-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/15/2023]
Abstract
Outbreaks of Microcystis blooms can affect growth of submerged plants, which in turn can inhibit cyanobacterial growth. Microcystin (MC)-producing and non-MC-producing Microcystis strains typically coexist in Microcystis-dominated blooms. However, the interaction between submerged plants and Microcystis at strain level is not clear. This study was aimed at assessing the effects of a submerged macrophyte Myriophyllum spicatum on one MC-producing versus one non-MC-producing strains of the cyanobacterium Microcystis using plant-Microcystis co-culture experiments. The impacts of Microcystis on M. spicatum were also examined. It showed that the MC-producing Microcystis strain had a higher resistance to negative impacts by the cocultured submerged plant M. spicatum than the non-MC-producing strain. By contrast, the plant M. spicatum was impacted more by the MC-producing Microcystis than the non-MC-producer. The associated bacterioplankton community was affected more by the MC-producing Microcystis than the cocultured M. spicatum. The MC cell quotas were significantly higher in the coculture treatment (the PM + treatment, p < 0.05), indicating that the production and release of MCs might be a key factor responsible for the reduced impact of M. spicatum. The higher concentrations of dissolved organic and reducing inorganic compounds might eventually exacerbate the recovering capacity of coexisting submerged plants. Overall, this study indicated that the capacity to produce MCs, as well as the density of Microcystis, should be taken into account when attempting to reestablish submerged vegetation to undertake remediation works.
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Affiliation(s)
- Yunni Gao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Hui Yang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Longfei Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xiaofei Gao
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Mei Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Jing Dong
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Man Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Jingxiao Zhang
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China
| | - Xuejun Li
- Engineering Lab of Henan Province for Aquatic Animal Disease Control, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, College of Fisheries, Henan Normal University, Xinxiang, 453007, China.
- Observation and Research Station On Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang, 474450, China.
| | - Zhiying Lu
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Michele A Burford
- Australian Rivers Institute, Griffith University, 170 Kessels Road, Nathan, QLD, 4111, Australia
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Cas9/gRNA-Mediated Mutations in PtrFLA40 and PtrFLA45 Reveal Redundant Roles in Modulating Wood Cell Size and SCW Synthesis in Poplar. Int J Mol Sci 2022; 24:ijms24010427. [PMID: 36613871 PMCID: PMC9820481 DOI: 10.3390/ijms24010427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) play an important role in plant development and adaptation to the environment. However, the roles of FLAs in wood formation remain poorly understood. Here, we identified a total of 50 PtrFLA genes in poplar. They were classified into four groups: A to D, among which group A was the largest group with 28 members clustered into four branches. Most PtrFLAs of group A were dominantly expressed in developing xylem based on microarray and RT-qPCR data. The roles of PtrFLA40 and PtrFLA45 in group A were investigated via the Cas9/gRNA-induced mutation lines. Loss of PtrFLA40 and PtrFLA45 increased stem length and diameter in ptrfla40ptrfla45 double mutants, but not in ptrfla40 or ptrfla45 single mutants. Further, our findings indicated that the ptrfla40ptrfla45 mutants enlarged the cell size of xylem fibers and vessels, suggesting a negative modulation in stem xylem cell size. In addition, wood lignin content in the ptrfla40fla45 mutants was increased by nearly 9%, and the lignin biosynthesis-related genes were significantly up-regulated in the ptrfla40fla45 mutants, in agreement with the increase in wood lignin content. Overall, Cas9/gRNA-mediated mutations in PtrFLA40 and PtrFLA45 reveal redundant roles in modulating wood cell size and secondary cell wall (SCW) synthesis in poplar.
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Tan Q, Yang Z, Xin X, Yang B, Xing Z, Li F, Zhang K, Tian Y, Zhu T. Serum periostin level is not sufficient to serve as a clinically applicable biomarker of osteoarthritis. BMC Musculoskelet Disord 2022; 23:1039. [PMID: 36451121 PMCID: PMC9714069 DOI: 10.1186/s12891-022-06017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Emerging knowledge has highlighted the role of periostin (POSTN) in osteoarthritis (OA) process; however, whether POSTN is suitable as a biomarker of OA remains unclear. This study aimed to investigate the potential value of POSTN as a biomarker of OA. METHODS Ten 6-month-old female Sprague-Dawley (SD) rats were used in this study. Five rats underwent ovariectomy (OVX) operation and the others were carried out sham operation. Thirty-two patients with OA and eighteen patients who had meniscus injuries or ligament injuries but with intact articular cartilages were recruited in this study from January to July 2019 at the Peking University International Hospital. We first detected the expression of POSTN in the cartilage of OVX induced OA rats and different compartments of the knee joint in patients with OA using immunohistochemistry. Besides, serum POSTN levels in patients with or without OA were examined using enzyme-linked immunosorbent assay (ELISA). The associations among serum POSTN levels, clinical symptoms, and radiological severity were assessed according to the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores and, Kellgren-Lawrence (KL) grading, respectively. Finally, multivariable cumulative link models were established to evaluate the validity of serum POSTN level as a predictor of knee OA. RESULTS The significantly higher POSTN expression was found in OVX-OA rats than Sham rats, while, the expression of POSTN was significantly higher in the torn cartilage of patients with OA. However, the serum POSTN level did not differ significantly between patients with and without OA. Additionally, we found no remarkable associations between serum POSTN level and WOMAC scores and KL grading. Subsequent analysis revealed that serum POSTN was not a significant predictor of OA. CONCLUSION Thus, although POSTN may be involved OA process and local POSTN is valuable in disease diagnosis and distinguishing of the severity of disease, its serum level is not sufficient to serve as a candidate biomarker of OA given the current analysis technology.
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Affiliation(s)
- Qizhao Tan
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.477019.cDepartment of Orthopaedics, Zibo Central Hospital, Zibo, Shandong, 255000 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China
| | - Zhongwei Yang
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China
| | - Xing Xin
- grid.449412.eDepartment of Orthopaedics, Peking University International Hospital, Beijing, 102206 P.R. China
| | - Bin Yang
- grid.449412.eDepartment of Orthopaedics, Peking University International Hospital, Beijing, 102206 P.R. China
| | - Zhili Xing
- grid.449412.eDepartment of Orthopaedics, Peking University International Hospital, Beijing, 102206 P.R. China
| | - Feng Li
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China
| | - Ke Zhang
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China ,grid.449412.eDepartment of Orthopaedics, Peking University International Hospital, Beijing, 102206 P.R. China
| | - Yun Tian
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China
| | - Tengjiao Zhu
- grid.411642.40000 0004 0605 3760Department of Orthopaedics, Peking University Third Hospital, Haidian District, 49 North Garden Road, Beijing, 100191 P.R. China ,grid.419897.a0000 0004 0369 313XEngineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing, P.R. China ,grid.449412.eDepartment of Orthopaedics, Peking University International Hospital, Beijing, 102206 P.R. China
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Kim D, Chong SH, Shin S, Ham S. Mutation effects on FAS1 domain 4 based on structure and solubility. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140746. [PMID: 34942360 DOI: 10.1016/j.bbapap.2021.140746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/07/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Mutations in the fasciclin 1 domain 4 (FAS1-4) of transforming growth factor β-induced protein (TGFBIp) are associated with insoluble extracellular deposits and corneal dystrophies (CDs). The decrease in solubility upon mutation has been implicated in CD; however, the exact molecular mechanisms are not well understood. Here, we performed molecular dynamics simulations followed by solvation thermodynamic analyses of the FAS1-4 domain and its three mutants-R555W, R555Q, and A546T-linked to granular corneal dystrophy type 1, Thiel-Behnke corneal dystrophy and lattice corneal dystrophy, respectively. We found that both R555W and R555Q mutants have less affinity toward solvent water relative to the wild-type protein. In the R555W mutant, a remarkable increase in solvation free energy was observed because of the structural changes near the mutation site. The mutation site W555 is buried in other hydrophobic residues, and R557 simultaneously forms salt bridges with E554 and D561. In the R555Q mutant, the increase in solvation free energy is caused by structural rearrangements far from the mutation site. R558 separately forms salt bridges with D575, E576, and E598. Thus, we thus identified the relationship between the decrease in solubility and conformational changes caused by mutations, which may be useful in designing potential therapeutics and in blocking FAS1 aggregation related to CD.
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Affiliation(s)
- DongGun Kim
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea; Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Song-Ho Chong
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Seokmin Shin
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea.
| | - Sihyun Ham
- Department of Chemistry, The Research Institute of Natural Sciences, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, Republic of Korea.
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Hwang S, Lee N, Choe D, Lee Y, Kim W, Kim JH, Kim G, Kim H, Ahn NH, Lee BH, Palsson BO, Cho BK. System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus. Front Bioeng Biotechnol 2022; 10:844200. [PMID: 35284422 PMCID: PMC8914203 DOI: 10.3389/fbioe.2022.844200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria belonging to Streptomyces have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in Streptomyces, system-level information remains limited. In this study, we integrated four multi-omics datasets from Streptomyces griseus NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3′-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5′-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in Streptomyces.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Neung-Ho Ahn
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Byoung-Hee Lee
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, South Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
- *Correspondence: Byung-Kwan Cho,
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10
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Song Y, Jiang CY, Liang ZL, Zhu HZ, Jiang Y, Yin Y, Qin YL, Huang HJ, Wang BJ, Wei ZY, Cheng RX, Liu ZP, Liu Y, Jin T, Wang AJ, Liu SJ. Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming. Appl Environ Microbiol 2021; 87:e0153421. [PMID: 34586909 PMCID: PMC8612268 DOI: 10.1128/aem.01534-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- The Ecology and Environment Branch of State Center for Research and Development of Oil Shale Exploitation, PetroChina Planning and Engineering Institute, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, China
| | - Ye Yin
- BGI-Qingdao, Qingdao, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zi-Yan Wei
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui-Xue Cheng
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, China
| | | | - Ai-Jie Wang
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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11
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Slonimskiy YB, Egorkin NA, Friedrich T, Maksimov EG, Sluchanko NN. Microalgal protein AstaP is a potent carotenoid solubilizer and delivery module with a broad carotenoid binding repertoire. FEBS J 2021; 289:999-1022. [PMID: 34582628 DOI: 10.1111/febs.16215] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
Carotenoids are lipophilic substances with many biological functions, from coloration to photoprotection. Being potent antioxidants, carotenoids have multiple biomedical applications, including the treatment of neurodegenerative disorders and retina degeneration. Nevertheless, the delivery of carotenoids is substantially limited by their poor solubility in the aqueous phase. Natural water-soluble carotenoproteins can facilitate this task, necessitating studies on their ability to uptake and deliver carotenoids. One such promising carotenoprotein, AstaP (astaxanthin-binding protein), was recently identified in eukaryotic microalgae, but its structure and functional properties remained largely uncharacterized. By using a correctly folded recombinant protein, here we show that AstaP is an efficient carotenoid solubilizer that can stably bind not only astaxanthin but also zeaxanthin, canthaxanthin, and, to a lesser extent, β-carotene, that is, carotenoids especially valuable to human health. AstaP accepts carotenoids provided as acetone solutions or embedded in membranes, forming carotenoid-protein complexes with an apparent stoichiometry of 1:1. We successfully produced AstaP holoproteins in specific carotenoid-producing strains of Escherichia coli, proving it is amenable to cost-efficient biotechnology processes. Regardless of the carotenoid type, AstaP remains monomeric in both apo- and holoform, while its rather minimalistic mass (~ 20 kDa) makes it an especially attractive antioxidant delivery module. In vitro, AstaP transfers different carotenoids to liposomes and to unrelated proteins from cyanobacteria, which can modulate their photoactivity and/or oligomerization. These findings expand the toolkit of the characterized carotenoid binding proteins and outline the perspective of the use of AstaP as a unique monomeric antioxidant nanocarrier with an extensive carotenoid binding repertoire.
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Affiliation(s)
- Yury B Slonimskiy
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nikita A Egorkin
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Thomas Friedrich
- Institute of Chemistry PC 14, Technical University of Berlin, Berlin, Germany
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
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12
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Role of a fasciclin domain protein in photooxidative stress and flocculation in Azospirillum brasilense Sp7. Res Microbiol 2021; 172:103875. [PMID: 34461275 DOI: 10.1016/j.resmic.2021.103875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 11/22/2022]
Abstract
Fasciclin domain proteins (FDP) are found in all domains of life, but their biological role and regulation are not clearly understood. While studying the proteome of a mutant (Car1) of Azospirillum brasilense Sp7 with a Tn5 insertion in the gene encoding an anti-sigma factor (ChrR1), we found that FDP was maximally expressed. To study the biological role of this FDP, we inactivated fdp in A. brasilense Sp7 and in its Car1 mutant, which rendered them sensitive to methylene blue (MB) and toluidine blue (TB) in the presence of light. The transcription of fdp was also strongly upregulated by an ECF sigma factor (RpoE1) and photooxidative stress. The fdp null mutants of A. brasilense Sp7 and its Car1 mutant produced relatively fewer carotenoids and showed reduced flocculation. The reduced ability of fdp null mutants to flocculate was partly due to their reduced ability to produce carotenoids as inhibition of carotenoid synthesis by diphenylamine reduced their flocculation ability by 15-20%. Hence, FDP plays an important role in protecting A. brasilense Sp7 against photo-oxidative stress by supporting carotenoid accumulation and cell aggregation.
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13
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Pathological Roles and Clinical Usefulness of Periostin in Type 2 Inflammation and Pulmonary Fibrosis. Biomolecules 2021; 11:biom11081084. [PMID: 34439751 PMCID: PMC8391913 DOI: 10.3390/biom11081084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Periostin is known to be a useful biomarker for various diseases. In this article, we focus on allergic diseases and pulmonary fibrosis, for which we and others are now developing detection systems for periostin as a biomarker. Biomarker-based precision medicine in the management of type 2 inflammation and fibrotic diseases since heterogeneity is of utmost importance. Periostin expression is induced by type 2 cytokines (interleukin-4/-13) or transforming growth factor-β, and plays a vital role in the pathogenesis of allergic inflammation or interstitial lung disease, respectively, andits serum levels are correlated disease severity, prognosis and responsiveness to the treatment. We first summarise the importance of type 2 biomarker and then describe the pathological role of periostin in the development and progression of type 2 allergic inflammation and pulmonary fibrosis. In addition, then, we summarise the recent development of assay methods for periostin detection, and analyse the diseases in which periostin concentration is elevated in serum and local biological fluids and its usefulness as a biomarker. Furthermore, we describe recent findings of periostin as a biomarker in the use of biologics or anti-fibrotic therapy. Finally, we describe the factors that influence the change in periostin concentration under the healthy conditions.
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14
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Seifert GJ. The FLA4-FEI Pathway: A Unique and Mysterious Signaling Module Related to Cell Wall Structure and Stress Signaling. Genes (Basel) 2021; 12:genes12020145. [PMID: 33499195 PMCID: PMC7912651 DOI: 10.3390/genes12020145] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023] Open
Abstract
Cell wall integrity control in plants involves multiple signaling modules that are mostly defined by genetic interactions. The putative co-receptors FEI1 and FEI2 and the extracellular glycoprotein FLA4 present the core components of a signaling pathway that acts in response to environmental conditions and insults to cell wall structure to modulate the balance of various growth regulators and, ultimately, to regulate the performance of the primary cell wall. Although the previously established genetic interactions are presently not matched by intermolecular binding studies, numerous receptor-like molecules that were identified in genome-wide interaction studies potentially contribute to the signaling machinery around the FLA4-FEI core. Apart from its function throughout the model plant Arabidopsis thaliana for the homeostasis of growth and stress responses, the FLA4-FEI pathway might support important agronomic traits in crop plants.
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Affiliation(s)
- Georg J Seifert
- Institute of Plant Biotechnology and Cell biology, University of Natural Resources and Life Science, Muthgasse 18, A-1190 Vienna, Austria
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15
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Liu E, MacMillan CP, Shafee T, Ma Y, Ratcliffe J, van de Meene A, Bacic A, Humphries J, Johnson KL. Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:615392. [PMID: 33362841 PMCID: PMC7758453 DOI: 10.3389/fpls.2020.615392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 05/19/2023]
Abstract
The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.
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Affiliation(s)
- Edgar Liu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Colleen P. MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Thomas Shafee
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | | | - Antony Bacic
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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16
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Suchan DM, Bergsveinson J, Manzon L, Pierce A, Kryachko Y, Korber D, Tan Y, Tambalo DD, Khan NH, Whiting M, Yost CK. Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots. Microb Genom 2020; 6:mgen000462. [PMID: 33151138 PMCID: PMC7725335 DOI: 10.1099/mgen.0.000462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023] Open
Abstract
The plant growth-promoting rhizobacterium Delftia acidovorans RAY209 is capable of establishing strong root attachment during early plant development at 7 days post-inoculation. The transcriptional response of RAY209 was measured using RNA-seq during early (day 2) and sustained (day 7) root colonization of canola plants, capturing RAY209 differentiation from a medium-suspended cell state to a strongly root-attached cell state. Transcriptomic data was collected in an identical manner during RAY209 interaction with soybean roots to explore the putative root colonization response to this globally relevant crop. Analysis indicated there is an increased number of significantly differentially expressed genes between medium-suspended and root-attached cells during early soybean root colonization relative to sustained colonization, while the opposite temporal pattern was observed for canola root colonization. Regardless of the plant host, root-attached RAY209 cells exhibited the least amount of differential gene expression between early and sustained root colonization. Root-attached cells of either canola or soybean roots expressed high levels of a fasciclin gene homolog encoding an adhesion protein, as well as genes encoding hydrolases, multiple biosynthetic processes, and membrane transport. Notably, while RAY209 ABC transporter genes of similar function were transcribed during attachment to either canola or soybean roots, several transporter genes were uniquely differentially expressed during colonization of the respective plant hosts. In turn, both canola and soybean plants expressed genes encoding pectin lyase and hydrolases - enzymes with purported function in remodelling extracellular matrices in response to RAY209 colonization. RAY209 exhibited both a core regulatory response and a planthost-specific regulatory response to root colonization, indicating that RAY209 specifically adjusts its cellular activities to adapt to the canola and soybean root environments. This transcriptomic data defines the basic RAY209 response as both a canola and soybean commercial crop and seed inoculant.
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Affiliation(s)
- Danae M. Suchan
- Department of Biology, University of Regina, Regina, SK, Canada
| | | | - Lori Manzon
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Alexa Pierce
- Department of Biology, University of Regina, Regina, SK, Canada
- Lallemand Plant Care North America, Saskatoon, SK, Canada
| | - Yuriy Kryachko
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Darren Korber
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yifang Tan
- Aquatic Crop Resource Development, National Research Council, Saskatoon, SK, Canada
| | | | - Nurul H. Khan
- Lallemand Plant Care North America, Saskatoon, SK, Canada
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17
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Jeong EL, Broad S, Moody R, Phillips-Jones M. The adherence-associated Fdp fasciclin I domain protein of the biohydrogen producer Rhodobacter sphaeroides is regulated by the global Prr pathway. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2020; 45:26840-26854. [PMID: 33093750 PMCID: PMC7561615 DOI: 10.1016/j.ijhydene.2020.07.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 05/23/2023]
Abstract
Expression of fdp, encoding a fasciclin I domain protein important for adherence in the hydrogen-producing bacterium Rhodobacter sphaeroides, was investigated under a range of conditions to gain insights into optimization of adherence for immobilization strategies suitable for H2 production. The fdp promoter was linked to a lacZ reporter and expressed in wild type and in PRRB and PRRA mutant strains of the Prr regulatory pathway. Expression was significantly negatively regulated by Prr under all conditions of aerobiosis tested including anaerobic conditions (required for H2 production), and aerobically regardless of growth phase, growth medium complexity or composition, carbon source, heat and cold shock and dark/light conditions. Negative fdp regulation by Prr was reflected in cellular levels of translated Fdp protein. Since Prr is required directly for nitrogenase expression, we propose optimization of Fdp-based adherence in R. sphaeroides for immobilized biohydrogen production by inactivation of the PrrA binding site(s) upstream of fdp.
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Affiliation(s)
- E.-L. Jeong
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - S.J. Broad
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - R.G. Moody
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - M.K. Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
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18
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All4894 encoding a novel fasciclin (FAS-1 domain) protein of Anabaena sp. PCC7120 revealed the presence of a thermostable β-glucosidase. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.102036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Shafee T, Bacic A, Johnson K. Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos. Mol Biol Evol 2020; 37:2155-2172. [DOI: 10.1093/molbev/msaa096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.
Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.
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Affiliation(s)
- Thomas Shafee
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
| | - Kim Johnson
- Department of Animal, Plant and Soil Sciences, La Trobe Institute for Agriculture & Food, La Trobe University, Melbourne, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou, China
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20
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Thiele W, Obermaier S, Müller M. A Fasciclin Protein Is Essential for Laccase-Mediated Selective Phenol Coupling in Sporandol Biosynthesis. ACS Chem Biol 2020; 15:844-848. [PMID: 32227858 DOI: 10.1021/acschembio.0c00025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biaryl scaffold, often showing axial chirality, is a common feature of various fungal natural products. Their biosynthesis requires an oxidative phenol-coupling reaction usually catalyzed by laccases, cytochrome P450 enzymes, or peroxidases. The combination of a laccase and a fasciclin domain-containing (fas) protein is encoded in many biosynthetic gene clusters of biaryls from ascomycetes. However, such phenol-coupling systems including their regio- and stereoselectivity have not been characterized so far. Elucidating the biosynthesis of the antiparasitic binaphthalene sporandol from Chrysosporium merdarium, we demonstrate the combination of a laccase and a fas protein to be crucial for the dimerization reaction. Only the heterologous coproduction of the laccase and the fas protein led to a functional phenol-coupling system, whereas the laccase alone showed no coupling activity. Thus, the laccase/fas protein combination forms an independent group of phenol-coupling enzymes that determines the coupling activity and selectivity of the reaction concurrently and applies to the biosynthesis of many fungal natural products with a biaryl scaffold.
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Affiliation(s)
- Wiebke Thiele
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Sebastian Obermaier
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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Tobias LM, Spokevicius AV, McFarlane HE, Bossinger G. The Cytoskeleton and Its Role in Determining Cellulose Microfibril Angle in Secondary Cell Walls of Woody Tree Species. PLANTS (BASEL, SWITZERLAND) 2020; 9:E90. [PMID: 31936868 PMCID: PMC7020502 DOI: 10.3390/plants9010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/28/2022]
Abstract
Recent advances in our understanding of the molecular control of secondary cell wall (SCW) formation have shed light on molecular mechanisms that underpin domestication traits related to wood formation. One such trait is the cellulose microfibril angle (MFA), an important wood quality determinant that varies along tree developmental phases and in response to gravitational stimulus. The cytoskeleton, mainly composed of microtubules and actin filaments, collectively contribute to plant growth and development by participating in several cellular processes, including cellulose deposition. Studies in Arabidopsis have significantly aided our understanding of the roles of microtubules in xylem cell development during which correct SCW deposition and patterning are essential to provide structural support and allow for water transport. In contrast, studies relating to SCW formation in xylary elements performed in woody trees remain elusive. In combination, the data reviewed here suggest that the cytoskeleton plays important roles in determining the exact sites of cellulose deposition, overall SCW patterning and more specifically, the alignment and orientation of cellulose microfibrils. By relating the reviewed evidence to the process of wood formation, we present a model of microtubule participation in determining MFA in woody trees forming reaction wood (RW).
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Affiliation(s)
- Larissa Machado Tobias
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Antanas V. Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
| | - Heather E. McFarlane
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria 3363, Australia; (A.V.S.); (G.B.)
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Chen SC, Weng CY, Lai MC, Tamaki H, Narihiro T. Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus. Mar Genomics 2019; 47:100673. [PMID: 30935830 DOI: 10.1016/j.margen.2019.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 11/25/2022]
Abstract
To date, the only methanoarchaea isolated directly from methane hydrate bearing sediments were Methanoculleus submarinus Nankai-1T and Methanoculleus sp. MH98A. Here, we provide the genome of Methanoculleus taiwanensis CYW4T isolated from the deep-sea subseafloor sediment at the Deformation Front offshore southwestern Taiwan, where methane hydrate deposits are likely located. Through comparative genomics analyses of nine Methanoculleus strains from various habitats, 2-3 coding genes for trehalose synthases were found in all nine Methanoculleus genomes, which were not detected in other methanogens and are therefore suggested as a signature of genus Methanoculleus among methane-producing archaea. In addition, the structural genes adjacent to trehalose synthase genes are comprised of the signaling module of Per-Arnt-Sim (PAS) domain-containing proteins, Hsp20 family proteins, arabinose efflux permeases and multiple surface proteins with fasciclin-like (FAS) repeat. This indicates that trehalose synthase gene clusters in Methanoculleus might play roles in the response to various stresses and regulate carbon storage and modification of surface proteins through accumulation of trehalose. The non-gas hydrate-associated Methanoculleus strains harbor carbon-monoxide dehydrogenase (cooS/acsA) genes, which are important for the conversion of acetate to methane at the step of CO oxidation/CO2 reduction in acetoclastic methanogens and further implies that these strains may be able to utilize CO for methanogenesis in their natural habitats. In addition, both genomes of M. bourgensis strains MS2T and MAB1 harbor highly abundant transposase genes, which may be disseminated from microbial communities in their habitats, sewage treatment plants and biogas reactors, which are breeding grounds for antibiotic resistance. Through comparative genomic analyses, we gained insight into understanding the life of strictly anaerobic methane-producing archaea in various habitats, especially in methane-based deep-sea ecosystems.
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Affiliation(s)
- Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Genome analysis of Rubritalea profundi SAORIC-165 T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean. J Microbiol 2019; 57:413-422. [PMID: 30806980 DOI: 10.1007/s12275-019-8712-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165T, a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.
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Dubé CD, Guiot SR. Characterization of the protein fraction of the extracellular polymeric substances of three anaerobic granular sludges. AMB Express 2019; 9:23. [PMID: 30729349 PMCID: PMC6367495 DOI: 10.1186/s13568-019-0746-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Extracellular polymeric substances (EPS) play major roles in the efficacy of biofilms such as anaerobic granules, ranging from structural stability to more specific functions. The EPS of three granular anaerobic sludges of different origins were studied and compared. Particularly, the peptides from the protein fraction were identified by mass spectrometry. Desulfoglaeba and Treponema bacterial genera and Methanosaeta and Methanobacterium archaeal genera were prominent in all three sludges. Methanosaeta concilii proteins were the most represented in EPS of all three sludges studied. Principally, four proteins found in the three sludges, the S-layer protein, the CO-methylating acetyl-CoA synthase, an ABC transporter substrate-binding protein and the methyl-coenzyme M reductase, were expressed by Methanosaeta concilii. Mainly catabolic enzymes were found from the 45 proteins identified in the protein fraction of EPS. This suggests that EPS may have a role in allowing extracellular catabolic reactions.
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Zheng Q, Lu J, Wang Y, Jiao N. Genomic reconstructions and potential metabolic strategies of generalist and specialist heterotrophic bacteria associated with an estuarySynechococcusculture. FEMS Microbiol Ecol 2019; 95:5303724. [DOI: 10.1093/femsec/fiz017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/26/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Jiayao Lu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, People's Republic of China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
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26
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Seifert GJ. Fascinating Fasciclins: A Surprisingly Widespread Family of Proteins that Mediate Interactions between the Cell Exterior and the Cell Surface. Int J Mol Sci 2018; 19:E1628. [PMID: 29857505 PMCID: PMC6032426 DOI: 10.3390/ijms19061628] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022] Open
Abstract
The Fasciclin 1 (FAS1) domain is an ancient structural motif in extracellular proteins present in all kingdoms of life and particularly abundant in plants. The FAS1 domain accommodates multiple interaction surfaces, enabling it to bind different ligands. The frequently observed tandem FAS1 arrangement might both positively and negatively regulate ligand binding. Additional protein domains and post-translational modifications are partially conserved between different evolutionary clades. Human FAS1 family members are associated with multiple aspects of health and disease. At the cellular level, mammalian FAS1 proteins are implicated in extracellular matrix structure, cell to extracellular matrix and cell to cell adhesion, paracrine signaling, intracellular trafficking and endocytosis. Mammalian FAS1 proteins bind to the integrin family of receptors and to protein and carbohydrate components of the extracellular matrix. FAS1 protein encoding plant genes exert effects on cellulosic and non-cellulosic cell wall structure and cellular signaling but to establish the modes of action for any plant FAS1 protein still requires biochemical experimentation. In fungi, eubacteria and archaea, the differential presence of FAS1 proteins in closely related organisms and isolated biochemical data suggest functions in pathogenicity and symbiosis. The inter-kingdom comparison of FAS1 proteins suggests that molecular mechanisms mediating interactions between cells and their environment may have evolved at the earliest known stages of evolution.
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Affiliation(s)
- Georg J Seifert
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Science, Muthgasse 18, 1190 Vienna, Austria.
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Turupcu A, Almohamed W, Oostenbrink C, Seifert GJ. A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms. PLANT SIGNALING & BEHAVIOR 2018; 13:e1507403. [PMID: 30148420 PMCID: PMC6204788 DOI: 10.1080/15592324.2018.1507403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 05/21/2023]
Abstract
The Arabidopsis thaliana Fasciclin like arabinogalactan protein 4 (FLA4) locus is required for normal root growth in a linear genetic pathway with the FEI1 and FEI2 loci coding for receptor-like kinases. The two Fas1 domains of FLA4 are conserved among angiosperms but only the C-terminal Fas1 domain is required for genetic function. We show that at low salt deletion of the N-terminal Fas1 domain of transgenic FLA4 leads to enhanced root elongation compared to the tandem Fas1 wild type version. Modeling the hypothetical interaction between FLA4 and FEI1 we show that the predicted interaction is predominantly involving the C-terminal Fas1 domain. Relative conformational mobility between the two FLA4 Fas1 domains might regulate the interaction with the FEI receptor kinases. We therefore speculate that the FLA4 FEI complex might be a sensor for environmental conditions in the apoplast.
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Affiliation(s)
- Aysegül Turupcu
- Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Wisam Almohamed
- Department for Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Georg J. Seifert
- Department for Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- CONTACT Georg J. Seifert Department for Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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28
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Landry NM, Cohen S, Dixon IMC. Periostin in cardiovascular disease and development: a tale of two distinct roles. Basic Res Cardiol 2017; 113:1. [PMID: 29101484 DOI: 10.1007/s00395-017-0659-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/12/2017] [Indexed: 12/18/2022]
Abstract
Tissue development and homeostasis are dependent upon the concerted synthesis, maintenance, and degradation of extracellular matrix (ECM) molecules. Cardiac fibrosis is now recognized as a primary contributor to incidence of heart failure, particularly heart failure with preserved ejection fraction, wherein cardiac filling in diastole is compromised. Periostin is a cell-associated protein involved in cell fate determination, proliferation, tumorigenesis, and inflammatory responses. As a non-structural component of the ECM, secreted 90 kDa periostin is emerging as an important matricellular factor in cardiac mesenchymal tissue development. In addition, periostin's role as a mediator in cell-matrix crosstalk has also garnered attention for its association with fibroproliferative diseases in the myocardium, and for its association with TGF-β/BMP signaling. This review summarizes the phylogenetic history of periostin, its role in cardiac development, and the major signaling pathways influencing its expression in cardiovascular pathology. Further, we provide a synthesis of the current literature to distinguish the multiple roles of periostin in cardiac health, development and disease. As periostin may be targeted for therapeutic treatment of cardiac fibrosis, these insights may shed light on the putative timing for application of periostin-specific therapies.
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Affiliation(s)
- Natalie M Landry
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Max Rady College of Medicine, Institute of Cardiovascular Sciences, University of Manitoba, Winnipeg, Canada
| | - Smadar Cohen
- Regenerative Medicine and Stem Cell Research Center, Ilse Katz Institute for Nanoscale Science and Technology, Beersheba, Israel.,Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ian M C Dixon
- Department of Physiology and Pathophysiology, Rady Faculty of Health Sciences, Max Rady College of Medicine, Institute of Cardiovascular Sciences, University of Manitoba, Winnipeg, Canada. .,Laboratory of Molecular Cardiology, St. Boniface Hospital Albrechtsen Research Centre, R3010-351 Taché Avenue, Winnipeg, MB R2H 2A6, Canada.
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29
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García-Castellanos R, Nielsen NS, Runager K, Thøgersen IB, Lukassen MV, Poulsen ET, Goulas T, Enghild JJ, Gomis-Rüth FX. Structural and Functional Implications of Human Transforming Growth Factor β-Induced Protein, TGFBIp, in Corneal Dystrophies. Structure 2017; 25:1740-1750.e2. [PMID: 28988748 DOI: 10.1016/j.str.2017.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/02/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
Abstract
A major cause of visual impairment, corneal dystrophies result from accumulation of protein deposits in the cornea. One of the proteins involved is transforming growth factor β-induced protein (TGFBIp), an extracellular matrix component that interacts with integrins but also produces corneal deposits when mutated. Human TGFBIp is a multi-domain 683-residue protein, which contains one CROPT domain and four FAS1 domains. Its structure spans ∼120 Å and reveals that vicinal domains FAS1-1/FAS1-2 and FAS1-3/FAS1-4 tightly interact in an equivalent manner. The FAS1 domains are sandwiches of two orthogonal four-stranded β sheets decorated with two three-helix insertions. The N-terminal FAS1 dimer forms a compact moiety with the structurally novel CROPT domain, which is a five-stranded all-β cysteine-knot solely found in TGFBIp and periostin. The overall TGFBIp architecture discloses regions for integrin binding and that most dystrophic mutations cluster at both molecule ends, within domains FAS1-1 and FAS1-4.
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Affiliation(s)
- Raquel García-Castellanos
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Nadia Sukusu Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Kasper Runager
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Marie V Lukassen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Ebbe T Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej, 10, 8000 Aarhus C, Denmark
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence), Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, c/Baldiri Reixac 15-21, 08028 Barcelona, Catalonia, Spain.
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30
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Ahn CS, Kim JG, Bae YA, Kim SH, Shin JH, Yang Y, Kang I, Kong Y. Fasciclin-calcareous corpuscle binary complex mediated protein-protein interactions in Taenia solium metacestode. Parasit Vectors 2017; 10:438. [PMID: 28931431 PMCID: PMC5606126 DOI: 10.1186/s13071-017-2359-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/31/2017] [Indexed: 01/30/2023] Open
Abstract
Background Neurocysticercosis (NC) caused by Taenia solium metacestode (TsM) is a serious neurological disease of global concern. Diverse bioactive molecules involved in the long-term survival of TsM might contribute to disease progression. Fasciclin (Fas) is an extracellular protein that mediates adhesion, migration and differentiation of cells by interacting with other molecules. We hypothesized that TsMFas might bind to calcareous corpuscle (CC) through its adhesive property and participate in crucial protein-protein interactions, thus contributing to the creation of a symbiotic interactome network. Methods Two paralogous TsMFas (TsMFas1 and TsMFas2) were isolated, and their molecular properties were characterized. The co-localization pattern of TsMFas1 and TsMFas2 with CC was determined. CC-TsMFas binary complex was generated by incubating CC with recombinant proteins (rTsMFas1 and 2). In vitro binding assay of CC-rTsMFas1 or CC-rTsMFas2 binary complex with TsM cellular proteins extracted from scolex and neck was conducted. Their binding partners were identified through proteomic analysis. Integrated protein-protein interaction networks were established. Results TsMFas1 (6072 bp long) was composed of 15 exons (841 amino acid polypeptide) interrupted by 14 introns. TsMFas2 (5201 bp long) comprised of 11 exons (597 amino acids) and 10 intervening introns. These proteins displayed 22% amino acid sequence identity to each other, but tightly conserved Fas-related domains. Several isoforms of Fas1 and Fas2 proteins might have been expressed through post-translational modifications. They showed adhesion activity with other cells. TsMFas proteins were largely distributed in parenchymal regions of the scolex and bladder wall. These molecules were co-localized with CC, a unique organelle found in platyhelminths. Subsequent proteome analysis of CC-Fas binary complex mediated protein-protein interactions revealed seven protein ligands in the TsM cellular proteins. Their functions were mainly segregated into carbohydrate metabolism (enolase, phosphoenolpyruvate carboxykinase, phosphoglycerate kinase and glyceraldehyde 3-phosphate dehydrogenase) and cytoskeleton/cellular motility (actin, paramyosin and innexin nuc-9). Those proteins had direct (physical) and/or indirect (functional) relationships along with their biochemical properties and biological roles. Conclusion Protein repertoires strongly suggest that TsMFas and CC may symbiotically mediate protein-protein interactions during biological processes to maintain efficacious homeostatic functions and ensure the prolonged survival of TsM in the host. Electronic supplementary material The online version of this article (10.1186/s13071-017-2359-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chun-Seob Ahn
- Department of Molecular Parasitology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Jeong-Geun Kim
- Department of Molecular Parasitology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Young-An Bae
- Department of Microbiology, Gachon University College of Medicine, Incheon, 21936, South Korea
| | - Seon-Hee Kim
- Department of Microbiology, Gachon University College of Medicine, Incheon, 21936, South Korea
| | - Joo-Ho Shin
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea
| | - Yichao Yang
- Guangxi Centers for Disease Prevention and Control, Nanning, Guangxi, 53002, China
| | - Insug Kang
- Department of Molecular Biology and Biochemistry, School of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Yoon Kong
- Department of Molecular Parasitology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.
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Xue H, Veit C, Abas L, Tryfona T, Maresch D, Ricardi MM, Estevez JM, Strasser R, Seifert GJ. Arabidopsis thaliana FLA4 functions as a glycan-stabilized soluble factor via its carboxy-proximal Fasciclin 1 domain. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:613-630. [PMID: 28482115 PMCID: PMC5575511 DOI: 10.1111/tpj.13591] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/28/2017] [Indexed: 05/12/2023]
Abstract
Fasciclin-like arabinogalactan proteins (FLAs) are involved in numerous important functions in plants but the relevance of their complex structure to physiological function and cellular fate is unresolved. Using a fully functional fluorescent version of Arabidopsis thaliana FLA4 we show that this protein is localized at the plasma membrane as well as in endosomes and soluble in the apoplast. FLA4 is likely to be GPI-anchored, is highly N-glycosylated and carries two O-glycan epitopes previously associated with arabinogalactan proteins. The activity of FLA4 was resistant against deletion of the amino-proximal fasciclin 1 domain and was unaffected by removal of the GPI-modification signal, a highly conserved N-glycan or the deletion of predicted O-glycosylation sites. Nonetheless these structural changes dramatically decreased endoplasmic reticulum (ER)-exit and plasma membrane localization of FLA4, with N-glycosylation acting at the level of ER-exit and O-glycosylation influencing post-secretory fate. We show that FLA4 acts predominantly by molecular interactions involving its carboxy-proximal fasciclin 1 domain and that its amino-proximal fasciclin 1 domain is required for stabilization of plasma membrane localization. FLA4 functions as a soluble glycoprotein via its carboxy-proximal Fas1 domain and its normal cellular trafficking depends on N- and O-glycosylation.
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Affiliation(s)
- Hui Xue
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Christiane Veit
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Lindy Abas
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Theodora Tryfona
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QWUK
| | - Daniel Maresch
- Department of ChemistryUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Martiniano M. Ricardi
- Biología Molecular y Neurociencias–Consejo Nacional de Investigaciones Científicas y Técnicas(IFIByNE‐CONICET)Instituto de FisiologíaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresC1428EGAArgentina
| | - José Manuel Estevez
- Biología Molecular y Neurociencias–Consejo Nacional de Investigaciones Científicas y Técnicas(IFIByNE‐CONICET)Instituto de FisiologíaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresC1428EGAArgentina
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos AiresBuenos Aires CPC1405BWEArgentina
| | - Richard Strasser
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
| | - Georg J. Seifert
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life ScienceBOKU ViennaMuthgasse 11A‐1190ViennaAustria
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Osman OA, Beier S, Grabherr M, Bertilsson S. Interactions of Freshwater Cyanobacteria with Bacterial Antagonists. Appl Environ Microbiol 2017; 83:e02634-16. [PMID: 28115385 PMCID: PMC5359482 DOI: 10.1128/aem.02634-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/07/2017] [Indexed: 01/15/2023] Open
Abstract
Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1:1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. l,d-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes.IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.
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Affiliation(s)
- Omneya Ahmed Osman
- Department of Ecology and Genetics, Limnology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Beier
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Manfred Grabherr
- Department of Medical Microbiology and Biochemistry, Bioinformatics Infrastructure for Life Sciences, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Verma S, Pandey S, Agarwal P, Verma P, Deshpande S, Saxena JK, Srivastava K, Chauhan PMS, Prabhakar YS. N-(7-Chloroquinolinyl-4-aminoalkyl)arylsulfonamides as antimalarial agents: rationale for the activity with reference to inhibition of hemozoin formation. RSC Adv 2016. [DOI: 10.1039/c6ra00846a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
New chloroquinolinyl arylsulfonamides with potential antimalarial activity inhibited hemozoin formation exceedingly well.
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Affiliation(s)
- Saroj Verma
- Medicinal and Process Chemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Shashi Pandey
- Medicinal and Process Chemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Pooja Agarwal
- Parasitology Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Pravesh Verma
- Biochemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Shreekant Deshpande
- Medicinal and Process Chemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Jitendra Kumar Saxena
- Biochemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Kumkum Srivastava
- Parasitology Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Prem M. S. Chauhan
- Medicinal and Process Chemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
| | - Yenamandra S. Prabhakar
- Medicinal and Process Chemistry Division
- Academy of Scientific and Innovative Research
- CSIR-Central Drug Research Institute
- Lucknow-226 031
- India
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Solution structure of the NDH-1 complex subunit CupS from Thermosynechococcus elongatus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1212-9. [DOI: 10.1016/j.bbabio.2015.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/30/2015] [Accepted: 05/06/2015] [Indexed: 11/20/2022]
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Rousseau JC, Sornay-Rendu E, Bertholon C, Garnero P, Chapurlat R. Serum periostin is associated with prevalent knee osteoarthritis and disease incidence/progression in women: the OFELY study. Osteoarthritis Cartilage 2015; 23:1736-42. [PMID: 26072384 DOI: 10.1016/j.joca.2015.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 04/28/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Our aim was to investigate the relationships between serum periostin (POSTN) and both prevalence and incidence/progression of knee osteoarthritis (OA) in women. METHODS We investigated 594 women (62.7 ± 11.2 yr) from the OFELY cohort. Knee radiographs were scored according to the Kellgren & Lawrence (KL) grading system at baseline and 4 years later. Spine, hip and hand OA were assessed at baseline. Prevalent knee OA was defined by a KL score higher or equal in 2. Progression of KL was defined as an increase of the KL score ≥1 during the 4 years follow-up. Serum POSTN was measured at baseline by ELISA. RESULTS By non-parametric tests, POSTN was significantly lower in 83 women with a KL score ≥2 at baseline, compared to those with a KL score <2 (n = 511; 1101 ± 300 vs 1181 ± 294 ng/ml, P = 0.002) after adjustment for age, body mass index (BMI), treatments and diseases, prevalent hand OA and prevalent lumbar spine OA. By logistic regression analyses, the odds-ratio of knee OA incidence/progression was significantly reduced by 21% (P = 0.043) for each quartile increase in serum POSTN at baseline, after adjustment for age, BMI, prevalent knee OA, prevalent hand OA and prevalent lumbar spine OA. CONCLUSIONS We show for the first time that serum POSTN is associated with prevalence and the risk of development/progression of knee OA in women.
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Affiliation(s)
- J C Rousseau
- INSERM Research Unit 1033, Université de Lyon, 69437 Lyon Cedex 03, France.
| | - E Sornay-Rendu
- INSERM Research Unit 1033, Université de Lyon, 69437 Lyon Cedex 03, France; Service de rhumatologie et pathologie osseuse, Hôpital E.-Herriot, Université de Lyon, 69437 Lyon Cedex 03, France.
| | - C Bertholon
- INSERM Research Unit 1033, Université de Lyon, 69437 Lyon Cedex 03, France.
| | - P Garnero
- INSERM Research Unit 1033, Université de Lyon, 69437 Lyon Cedex 03, France; Cisbio Bioassays, Codolet, France; Service de rhumatologie et pathologie osseuse, Hôpital E.-Herriot, Université de Lyon, 69437 Lyon Cedex 03, France.
| | - R Chapurlat
- INSERM Research Unit 1033, Université de Lyon, 69437 Lyon Cedex 03, France; Service de rhumatologie et pathologie osseuse, Hôpital E.-Herriot, Université de Lyon, 69437 Lyon Cedex 03, France.
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A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation. J Bacteriol 2015; 197:3446-55. [PMID: 26283770 DOI: 10.1128/jb.00420-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/13/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cell shape has been suggested to play an important role in the regulation of bacterial attachment to surfaces and the formation of communities associated with surfaces. We found that a cardiolipin synthase (Δcls) mutant of the rod-shaped bacterium Rhodobacter sphaeroides--in which synthesis of the anionic, highly curved phospholipid cardiolipin (CL) is reduced by 90%--produces ellipsoid-shaped cells that are impaired in biofilm formation. Reducing the concentration of CL did not cause significant defects in R. sphaeroides cell growth, swimming motility, lipopolysaccharide and exopolysaccharide production, surface adhesion protein expression, and membrane permeability. Complementation of the CL-deficient mutant by ectopically expressing CL synthase restored cells to their rod shape and increased biofilm formation. Treating R. sphaeroides cells with a low concentration (10 μg/ml) of the small-molecule MreB inhibitor S-(3,4-dichlorobenzyl)isothiourea produced ellipsoid-shaped cells that had no obvious growth defect yet reduced R. sphaeroides biofilm formation. This study demonstrates that CL plays a role in R. sphaeroides cell shape determination, biofilm formation, and the ability of the bacterium to adapt to its environment. IMPORTANCE Membrane composition plays a fundamental role in the adaptation of many bacteria to environmental stress. In this study, we build a new connection between the anionic phospholipid cardiolipin (CL) and cellular adaptation in Rhodobacter sphaeroides. We demonstrate that CL plays a role in the regulation of R. sphaeroides morphology and is important for the ability of this bacterium to form biofilms. This study correlates CL concentration, cell shape, and biofilm formation and provides the first example of how membrane composition in bacteria alters cell morphology and influences adaptation. This study also provides insight into the potential of phospholipid biosynthesis as a target for new chemical strategies designed to alter or prevent biofilm formation.
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Mosher DF, Johansson MW, Gillis ME, Annis DS. Periostin and TGF-β-induced protein: Two peas in a pod? Crit Rev Biochem Mol Biol 2015; 50:427-39. [PMID: 26288337 DOI: 10.3109/10409238.2015.1069791] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Periostin (PN) and TGF-β-induced protein (βig-h3) are paralogs that contain a single emilin and four fasciclin-1 modules and are secreted from cells. PN receives attention because of its up-regulation in cancer and degenerative and allergic diseases. βig-h3 is highly enriched in cornea and best known for harboring mutations in humans associated with corneal dystrophies. Both proteins are expressed widely, and many functions, some over-lapping, have been attributed to PN and βig-h3 based on biochemical, cell culture, and whole animal experiments. We attempt to organize this knowledge so as to facilitate research on these interesting and incompletely understood proteins. We focus particularly on whether PN and βig-h3 are modified by vitamin K-dependent γ-glutamyl carboxylation, a question of considerable importance given the profound effects of γ-carboxylation on structure and function of other proteins. We consider the roles of PN and βig-h3 in formation of extracellular matrix and as ligands for integrin receptors. We attempt to reconcile the contradictory results that have arisen concerning the role of PN, which has emerged as a marker of TH2 immunity, in murine models of allergic asthma. Finally, when possible we compare and contrast the structures and functions of the two proteins.
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Affiliation(s)
- Deane F Mosher
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , USA
| | - Mats W Johansson
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , USA
| | - Mary E Gillis
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , USA
| | - Douglas S Annis
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , USA
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MacMillan CP, Taylor L, Bi Y, Southerton SG, Evans R, Spokevicius A. The fasciclin-like arabinogalactan protein family of Eucalyptus grandis contains members that impact wood biology and biomechanics. THE NEW PHYTOLOGIST 2015; 206:1314-27. [PMID: 25676073 DOI: 10.1111/nph.13320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/19/2014] [Indexed: 05/21/2023]
Abstract
Fasciclin-like arabinogalactan protein (FLA) families have been identified and characterised in key plant species, with some members exhibiting functional specialization. Here we identify the FLA family of Eucalyptus grandis, and investigate the roles of three single-FAS domain FLAs, with particular focus on secondary cell-wall formation and wood properties. We use various in-silico approaches to identify and characterise E. grandis genome FLAs, and perform phylogenetic comparisons with other species. For three key FLAs, we perform functional testing including promoter-reporter and overexpression transgenic approaches using eucalypts, poplar and tobacco. Of the 18 eucalypt FLAs identified, several were specifically and highly expressed in stems. The specificity to stem xylem vessel and fibre development was demonstrated with EniFLA1promoter:GUS studies in several species. Testing of select eucalypt FLAs resulted in altered wood development and properties, for example 35S:EgrFLA2 led to a 3 degree reduction in cellulose microfibril angle in eucalypt xylem fibres, and 35S:EgrFLA3 to a reduction in tobacco stem flexural strength. These results indicate that the eucalypt FLA family contains diverse members, and particular members with single FAS domains that are functionally specialized for secondary cell wall growth and properties.
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Affiliation(s)
| | - Lynette Taylor
- Department of Forest and Ecosystem Science, The University of Melbourne, Water Street, Creswick, VIC, 3363, Australia
| | - Yingdong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | | | - Rob Evans
- The University of Melbourne, Burnley Campus, 500 Yarra Boulevard, Richmond, VIC, 3121, Australia
| | - Antanas Spokevicius
- Department of Forest and Ecosystem Science, The University of Melbourne, Water Street, Creswick, VIC, 3363, Australia
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Abstract
As FEBS celebrates its 50th anniversary, it also marks the launch 3 years ago of its newest journal, FEBS Open Bio. This online-only open access journal is now indexed in Web of Science. Papers originally submitted to The FEBS Journal can be transferred to FEBS Open Bio together with any reviewer reports, offering authors a fast-track alternative for publication of their work.
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Affiliation(s)
- Mary Purton
- FEBS Open Bio Editorial Office, Cambridge, UK
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Seifert GJ, Xue H, Acet T. The Arabidopsis thaliana FASCICLIN LIKE ARABINOGALACTAN PROTEIN 4 gene acts synergistically with abscisic acid signalling to control root growth. ANNALS OF BOTANY 2014; 114:1125-33. [PMID: 24603604 PMCID: PMC4195540 DOI: 10.1093/aob/mcu010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS The putative FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 4 (At-FLA4) locus of Arabidopsis thaliana has previously been shown to be required for the normal growth of wild-type roots in response to moderately elevated salinity. However, the genetic and physiological pathway that connects At-FLA4 and normal root growth remains to be elucidated. METHODS The radial swelling phenotype of At-fla4 was modulated with growth regulators and their inhibitors. The relationship of At-FLA4 to abscisic acid (ABA) signalling was analysed by probing marker gene expression and the observation of the At-fla4 phenotype in combination with ABA signalling mutants. KEY RESULTS Application of ABA suppresses the non-redundant role of At-FLA4 in the salt response. At-FLA4 positively regulates the response to low ABA concentration in roots and is required for the normal expression of ABA- and abiotic stress-induced genes. The At-fla4 phenotype is enhanced in the At-abi4 background, while two genetic suppressors of ABA-induced gene expression are required for salt oversensitivity of At-fla4. Salt oversensitivity in At-fla4 is suppressed by the CYP707A inhibitor abscinazole E2B, and salt oversensitivity in At-fla4 roots is phenocopied by chemical inhibition of ABA biosynthesis. CONCLUSIONS The predicted lipid-anchored glycoprotein At-FLA4 positively regulates cell wall biosynthesis and root growth by modulating ABA signalling.
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Affiliation(s)
- Georg J Seifert
- University of Natural Resources and Life Science, Vienna, Austria; Department of Applied Genetics and Cell Biology, Muthgasse 18, A-1990 Vienna, Austria
| | - Hui Xue
- University of Natural Resources and Life Science, Vienna, Austria; Department of Applied Genetics and Cell Biology, Muthgasse 18, A-1990 Vienna, Austria
| | - Tuba Acet
- University of Natural Resources and Life Science, Vienna, Austria; Department of Applied Genetics and Cell Biology, Muthgasse 18, A-1990 Vienna, Austria Gümüşhane University, School of Health & Nursing, 29100 Gümüşhane, Turkey Karadeniz Technical University, Science Faculty, Department of Biology, 61080 Trabzon, Turkey
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Association of serum periostin with aspirin-exacerbated respiratory disease. Ann Allergy Asthma Immunol 2014; 113:314-20. [PMID: 25037608 DOI: 10.1016/j.anai.2014.06.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 05/21/2014] [Accepted: 06/20/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Recent studies recommend periostin as a systemic biomarker of eosinophilic airway inflammation to predict responses to novel treatments that targets eosinophilic TH2-driven inflammation in asthmatic patients. OBJECTIVE To investigate the clinical implications of serum periostin levels in patients with aspirin-exacerbated respiratory disease (AERD) based on its overlapping TH2-mediated pathogenesis with the eosinophilic asthma. METHODS Serum periostin levels were measured by human periostin enzyme-linked immunosorbent assay (ELISA) in serum samples from 277 adults with asthma. Serum periostin levels were compared between patients with AERD and aspirin tolerant asthma (ATA) with other asthma phenotypes, such as severe or nonsevere asthma and eosinophilic or noneosinophilic asthma. The association of serum periostin levels with clinical parameters (including disease severity and comorbid condition) was analyzed. RESULTS Serum periostin levels were significantly higher in patients with AERD vs ATA, patients with severe asthma vs nonsevere asthma, and patients with eosinophilic asthma vs noneosinophilic asthma (P=.005, P=.02, and P=.001, respectively). Multivariate regression analysis revealed serum periostin levels as a significant parameter to predict AERD phenotype (P=.006) together with severe asthma phenotype (P=.04). In addition, serum periostin levels correlated with blood eosinophil counts (Spearman ñ = 0.244, P<.001) and sputum eosinophil counts (Spearman ñ = 0.261, P < 0.001). Higher serum periostin levels were noted in comorbid AERD patients with more severe chronic rhinosinusitis (Lund-Mackay stages 3 and 4) than those with less severe chronic rhinosinusitis (Lund-Mackay stages 1 and 2) (P = .03). CONCLUSION Serum periostin levels are significantly elevated in AERD patients and associated with AERD phenotype and disease severity.
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Hwang EY, Jeong MS, Park EK, Kim JH, Jang SB. Structural characterization and interaction of periostin and bone morphogenetic protein for regulation of collagen cross-linking. Biochem Biophys Res Commun 2014; 449:425-31. [PMID: 24858685 DOI: 10.1016/j.bbrc.2014.05.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/14/2014] [Indexed: 11/19/2022]
Abstract
Periostin appears to be a unique extracellular protein secreted by fibroblasts that is upregulated following injury to the heart or changes in the environment. Periostin has the ability to associate with other critical extracellular matrix (ECM) regulators such as TGF-β, tenascin, and fibronectin, and is a critical regulator of fibrosis that functions by altering the deposition and attachment of collagen. Periostin is known to be highly expressed in carcinoma cells, but not in normal breast tissues. The protein has a structural similarity to insect fasciclin-1 (Fas 1) and can be induced by transforming growth factor-β (TGF-β) and bone morphogenetic protein (BMP)-2. To investigate the molecular interaction of periostin and bone morphogenetic protein, we modeled these three-dimensional structures and their binding sites. We demonstrated direct interaction between periostin and BMP1/2 in vitro using several biochemical and biophysical assays. We found that the structures of the first, second, and fourth Fas1 domains in periostin are similar to that of the fourth Fas 1 domain of TGFBIp. However, the structure of the third Fas 1 domain in periostin is different from those of the first, second, and fourth Fas1 domains, while it is similar to the NMR structure of Fasciclin-like protein from Rhodobacter sphaeroides. These results will useful in further functional analysis of the interaction of periostin and bone morphogenetic protein.
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Affiliation(s)
- Eun Young Hwang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea
| | - Mi Suk Jeong
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea
| | - Eun-Kyeong Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea
| | - Jae Ho Kim
- Department of Physiology, College of Medicine, Pusan National University, Busan 602-735, Republic of Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 609-735, Republic of Korea.
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Tran VT, Braus-Stromeyer SA, Kusch H, Reusche M, Kaever A, Kühn A, Valerius O, Landesfeind M, Aßhauer K, Tech M, Hoff K, Pena-Centeno T, Stanke M, Lipka V, Braus GH. Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots. THE NEW PHYTOLOGIST 2014; 202:565-581. [PMID: 24433459 DOI: 10.1111/nph.12671] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/03/2013] [Indexed: 05/05/2023]
Abstract
Six transcription regulatory genes of the Verticillium plant pathogen, which reprogrammed nonadherent budding yeasts for adhesion, were isolated by a genetic screen to identify control elements for early plant infection. Verticillium transcription activator of adhesion Vta2 is highly conserved in filamentous fungi but not present in yeasts. The Magnaporthe grisea ortholog conidiation regulator Con7 controls the formation of appressoria which are absent in Verticillium species. Vta2 was analyzed by using genetics, cell biology, transcriptomics, secretome proteomics and plant pathogenicity assays. Nuclear Vta2 activates the expression of the adhesin-encoding yeast flocculin genes FLO1 and FLO11. Vta2 is required for fungal growth of Verticillium where it is a positive regulator of conidiation. Vta2 is mandatory for accurate timing and suppression of microsclerotia as resting structures. Vta2 controls expression of 270 transcripts, including 10 putative genes for adhesins and 57 for secreted proteins. Vta2 controls the level of 125 secreted proteins, including putative adhesins or effector molecules and a secreted catalase-peroxidase. Vta2 is a major regulator of fungal pathogenesis, and controls host-plant root infection and H2 O2 detoxification. Verticillium impaired in Vta2 is unable to colonize plants and induce disease symptoms. Vta2 represents an interesting target for controlling the growth and development of these vascular pathogens.
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Affiliation(s)
- Van-Tuan Tran
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
- Department of Microbiology, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Susanna A Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Michael Reusche
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
| | - Alexander Kaever
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Anika Kühn
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Manuel Landesfeind
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Kathrin Aßhauer
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Maike Tech
- Department of Bioinformatics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Goldschmidtstr. 1, D-37077, Göttingen, Germany
| | - Katharina Hoff
- Institute for Mathematics and Computer Science, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Straße 47, D-17487, Greifswald, Germany
| | - Tonatiuh Pena-Centeno
- Institute for Mathematics and Computer Science, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Straße 47, D-17487, Greifswald, Germany
| | - Mario Stanke
- Institute for Mathematics and Computer Science, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Straße 47, D-17487, Greifswald, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077, Göttingen, Germany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
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Strabala TJ, Macmillan CP. The Arabidopsis wood model-the case for the inflorescence stem. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 210:193-205. [PMID: 23849126 DOI: 10.1016/j.plantsci.2013.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 05/09/2013] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Arabidopsis thaliana has successfully served as a model to discover genes and proteins that have roles in a wide range of plant traits, including wood-related traits, such as lignin, cellulose and hemicellulose biosynthesis, secondary growth regulation, and secondary cell wall synthesis. Both the radially thickened hypocotyl and the inflorescence stem (flower stalk) have been studied. In this review, we address lingering doubts regarding the utility of Arabidopsis as a model for wood development by highlighting studies that provide new biochemical and biophysical evidence that extend support for the Arabidopsis inflorescence stem as a model for wood development beyond what is currently thought. We describe different aspects of Arabidopsis that make it a highly versatile tool for the study of wood development. One would likely utilise the radially thickened hypocotyl because of its more fully developed vascular cambium for traits related specifically to secondary (i.e. cambial) growth. It is more productive to utilise the inflorescence stem for wood-like biophysical traits. Accession variation has been underexploited as a powerful method to discover genes governing wood-like traits. We discuss recent findings that survey the accession variation in Arabidopsis for biochemical and biophysical properties of various wood traits, such as microfibril angle, tensile strength and cellulose/hemicellulose content. Furthermore we discuss how larger-scale studies of this nature using plants grown in long days (as opposed to the current short-day paradigm) could accelerate gene discovery and our understanding of cell wall and wood development. We highlight some relatively unexplored areas of research relating to the secondary cell wall composition, architecture and biophysical properties of the inflorescence stem, and how these traits are relevant to wood formation. The Arabidopsis inflorescence stem has other characteristics, expressed genes and traits held in common with woody species that have not been widely characterised or discussed to date. We discuss how this conservation may indicate the more general potential for "true" woodiness in herbaceous species, in the context of so-called secondary woodiness.
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