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Das Laha S, Das D, Ghosh T, Podder S. Enrichment of intrinsically disordered residues in ohnologs facilitates abiotic stress resilience in Brassica rapa. JOURNAL OF PLANT RESEARCH 2023; 136:239-251. [PMID: 36607467 DOI: 10.1007/s10265-022-01432-6] [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: 11/18/2021] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis thaliana and Brassica rapa are in the same evolutionary lineage, although the latter experienced an additional whole genome triplication event. Therefore, it would be intriguing to investigate the traits that gene duplication imposes to mediate plant stress tolerance. Here, we noticed that B. rapa abiotic stress resistance (ASR) genes which code at least one stress responsive domain have a significantly higher number of paralogs than A. thaliana. Analysing the disordered content of the ASR genes in both species, we found that intrinsically disordered residues (IDR) are specifically enriched in whole genome duplication (WGD) derived paralogs. Subsequently, domain similarity analysis between WGD pairs of both species has revealed that majority of WGD pairs in B. rapa did not share domains with each other. Furthermore, domain enrichment analysis has shown that B. rapa paralogs contain 36 distinct stress responsive enriched domains, significantly higher than A. thaliana paralogs. Next, we performed MSA to investigate the domain conservation between orthologs and ohnologs pairs, we found that 80.13% of B. rapa ohnologs acquire new domains, depicting the fact that ohnologs play a significant role in stress-related behaviours. The average IDR content of the ohnologs enriching new domains after gene duplication in B. rapa (0.19), is also significantly higher than A. thaliana (0.04). Interestingly, we also found that all of these attributes i.e., exhibiting higher number of WGD paralogs and enhancement of IDR in ASR genes of B. rapa compared to A. thaliana is exclusive for ASR genes only. No such significant differences were observed in randomly selected non-ASR genes between the two species. Together these results provide strong support for the hypothesis that augmentation of IDR content followed by a whole genome duplication event imposes the stress resistance potentiality in B. rapa. This research will shed light on the mechanism of how B. rapa is able to successfully adapt to stress over the evolutionary timescale.
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Affiliation(s)
- Shayani Das Laha
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
| | - Deepyaman Das
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
| | - Tapash Ghosh
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
- Department of Bioinformatics, Bose Institute, Kolkata, West Bengal, India
| | - Soumita Podder
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India.
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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Kim J, Lee H, Lee HG, Seo PJ. Get closer and make hotspots: liquid-liquid phase separation in plants. EMBO Rep 2021; 22:e51656. [PMID: 33913240 DOI: 10.15252/embr.202051656] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) facilitates the formation of membraneless compartments in a cell and allows the spatiotemporal organization of biochemical reactions by concentrating macromolecules locally. In plants, LLPS defines cellular reaction hotspots, and stimulus-responsive LLPS is tightly linked to a variety of cellular and biological functions triggered by exposure to various internal and external stimuli, such as stress responses, hormone signaling, and temperature sensing. Here, we provide an overview of the current understanding of physicochemical forces and molecular factors that drive LLPS in plant cells. We illustrate how the biochemical features of cellular condensates contribute to their biological functions. Additionally, we highlight major challenges for the comprehensive understanding of biological LLPS, especially in view of the dynamic and robust organization of biochemical reactions underlying plastic responses to environmental fluctuations in plants.
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Affiliation(s)
- Jiwoo Kim
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H. A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana. Cell Commun Signal 2021; 19:38. [PMID: 33761918 PMCID: PMC7992989 DOI: 10.1186/s12964-021-00718-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. Methods A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. Results Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. Conclusions These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. ![]()
Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00718-x.
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Affiliation(s)
- Hui Shao
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Wenmin Huang
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Luisana Avilan
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | | | - Carine Puppo
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Rémy Puppo
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Régine Lebrun
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Brigitte Gontero
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
| | - Hélène Launay
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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Knox-Brown P, Rindfleisch T, Günther A, Balow K, Bremer A, Walther D, Miettinen MS, Hincha DK, Thalhammer A. Similar Yet Different-Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins. Int J Mol Sci 2020; 21:E2794. [PMID: 32316452 PMCID: PMC7215670 DOI: 10.3390/ijms21082794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.
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Affiliation(s)
- Patrick Knox-Brown
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Tobias Rindfleisch
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
| | - Anne Günther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Kim Balow
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anne Bremer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
- Department for Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Dirk Walther
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Markus S. Miettinen
- Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, D-14476 Potsdam, Germany;
| | - Dirk K. Hincha
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany; (A.G.); (K.B.); (A.B.); (D.W.); (D.K.H.)
| | - Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24–25, D-14476 Potsdam, Germany; (P.K.-B.); (T.R.)
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Common Functions of Disordered Proteins across Evolutionary Distant Organisms. Int J Mol Sci 2020; 21:ijms21062105. [PMID: 32204351 PMCID: PMC7139818 DOI: 10.3390/ijms21062105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
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Zhou J, Oldfield CJ, Yan W, Shen B, Dunker AK. Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. Protein Sci 2019; 28:1652-1663. [PMID: 31299122 DOI: 10.1002/pro.3680] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/29/2019] [Accepted: 07/03/2019] [Indexed: 02/05/2023]
Abstract
Disordered domains are long regions of intrinsic disorder that ideally have conserved sequences, conserved disorder, and conserved functions. These domains were first noticed in protein-protein interactions that are distinct from the interactions between two structured domains and the interactions between structured domains and linear motifs or molecular recognition features (MoRFs). So far, disordered domains have not been systematically characterized. Here, we present a bioinformatics investigation of the sequence-disorder-function relationships for a set of probable disordered domains (PDDs) identified from the Pfam database. All the Pfam seed proteins from those domains with at least one PDD sequence were collected. Most often, if a set contains one PDD sequence, then all members of the set are PDDs or nearly so. However, many seed sets have sequence collections that exhibit diverse proportions of predicted disorder and structure, thus giving the completely unexpected result that conserved sequences can vary substantially in predicted disorder and structure. In addition to the induction of structure by binding to protein partners, disordered domains are also induced to form structure by disulfide bond formation, by ion binding, and by complex formation with RNA or DNA. The two new findings, (a) that conserved sequences can vary substantially in their predicted disorder content and (b) that homologues from a single domain can evolve from structure to disorder (or vice versa), enrich our understanding of the sequence ➔ disorder ensemble ➔ function paradigm.
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Affiliation(s)
- Jianhong Zhou
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | | | - Wenying Yan
- School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
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