Structural and functional analysis of SMO-1, the SUMO homolog in Caenorhabditis elegans

Surana, Parag; Gowda, Chandrakala M; Tripathi, Vasvi; Broday, Limor; Das, Ranabir

doi:10.1371/journal.pone.0186622

Cited by 10 publications

(9 citation statements)

References 56 publications

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“…In mammals, SUMO-2, unlike SUMO-1, can assemble poly-SUMO chains on different substrates in the same protein. For SMO-1, such poly-SUMO chain formation has not been reported in vivo, although poly-SMO-1 chains were observed in-vitro (Surana et al, 2017). These poly-SUMO chains were implicated in recruiting other proteins to give rise to more complex interactions (Psakhye et al, 2019).…”

Section: Introductionmentioning

confidence: 96%

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SUMOylation of the chromodomain factor MRG-1 inC. elegansaffects chromatin-regulatory dynamics

Baytek

Blume

Demirel

et al. 2021

Preprint

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Epigenetic mechanisms to control chromatin accessibility and structure is important for gene expression in eukaryotic cells. Chromatin regulation ensures proper development and cell fate specification but is also essential later in life. Modifications of histone proteins as an integral component of chromatin can promote either gene expression or repression, respectively. Proteins containing specific domains such as the chromodomain recognize mono-, di- or tri-methylated lysine residues on histone H3. The chromodomain protein MRG-1 in Caenorhabditis elegans is the ortholog of mammalian MRG15, which belongs to the MORF4 Related Gene (MRG) family in humans. In C. elegans MRG-1 predominantly binds methylated histone H3 lysine residues at position 36 (H3K36me3). MRG-1 is important during germline maturation and for safeguarding the germ cell identity. However, it lacks enzymatic activity and depends on protein-protein interaction to cooperate with other factors to regulate chromatin. To elucidate the variety of MRG-1 interaction partners we performed in-depth protein-protein interaction analysis using immunoprecipitations coupled with mass-spectrometry. Besides previously described and novel interactions with other proteins, we also detected a strong association with the Small Ubiquitin-like Modifier (SUMO). Since SUMO is known to be attached to proteins in order to modulate the target proteins activity we assessed whether MRG-1 is post-translationally modified by SUMOylation. Notably, we provide evidence that MRG-1 is indeed SUMOylated and that this post-translational modification influences the chromatin-binding profile of MRG-1 in the C. elegans genome. Our presented study hints towards an important role of SUMOylation in the context of epigenetic regulation via the chromodomain protein MRG-1, which may be a conserved phenomenon also in mammalian species.

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Section: Introductionmentioning

confidence: 96%

“…These enzymes consist of an E1 (AOS-1/UBA-2), an E2 (UBC-9), several E3 ligases . Unlike vertebrates and some plants, C. elegans expresses only a single SUMO protein, SMO-1 (Surana et al, 2017). In mammals, SUMO-2, unlike SUMO-1, can assemble poly-SUMO chains on different substrates in the same protein.…”

Section: Introductionmentioning

confidence: 99%

SUMOylation of the chromodomain factor MRG-1 inC. elegansaffects chromatin-regulatory dynamics

Baytek

Blume

Demirel

et al. 2021

Preprint

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“…Examination on the genes in this cluster found that the elevation of certain genes could repress the variant formation in C. elegans . For example, SMO family genes play important role in repairing DNA damage, 54 SMO‐1 modification on the ubiquitin E3 HERC2 triggers recruitment of further repair factors at DNA repair foci, including the ubiquitin E3 BRCA1/BARD1 55 ; POS‐1 has an important role in regulating the expression of maternal mRNAs in germline blastomeres, and mutations in pos‐1 cause several defects in the development of the germline blastomeres 56 ; PUF RNA‐binding proteins (RNABPs), PUF‐3/11 and PUF‐5/6/7, control different specific aspects of oocyte formation: silencing PUF‐3/‐11 via RNAi yielded an embryonic lethal phenotype, 57 whereas depletion of PUF‐5 and PUF‐6/7 together caused defects in oocyte formation and early embryonic cell divisions 58 . Our results suggest that DNA damage might occur in the reproduction system of C. elegans during bacterial infection.…”

Section: Resultsmentioning

confidence: 99%

Organism dual RNA‐seq reveals the importance of BarA/UvrY inVibrio parahaemolyticusvirulence

Zhang¹,

Xie²,

Zhang³

et al. 2020

FASEB j.

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Elucidation of host‐pathogen interaction is essential for developing effective strategies to combat bacterial infection. Dual RNA‐Seq using cultured cells or tissues/organs as the host of pathogen has emerged as a novel strategy to understand the responses concurrently from both pathogen and host at cellular level. However, bacterial infection mostly causes systematic responses from the host at organism level where the interplay is urgently to be understood but inevitably being neglected by the current practice. Here, we developed an approach that simultaneously monitor the genome‐wide infection‐linked transcriptional alterations in both pathogenic Vibrio parahaemolyticus and the infection host nematode Caenorhabditis elegans. Besides the dynamic alterations in transcriptomes of both C. elegans and V. parahaemolyticus during infection, we identify a two‐component system, BarA/UvrY, that is important for virulence in host. BarA/UvrY not only controls the virulence factors in V. parahaemolyticus including Type III and Type VI secretion systems, but also attenuates innate immune responses in C. elegans, including repression on the MAP kinase‐mediated cascades. Thus, our study exemplifies the use of dual RNA‐Seq at organism level to uncover previously unrecognized interplay between host and pathogen.

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“…This could be due to a lack of extensive characterization of conformational flexibility of native‐state in SUMO systems. Native‐state landscape of ubiquitin has been explored both by experimental as well as computational means, but only a few such reports are available in case of SUMO proteins …”

Section: Introductionmentioning

confidence: 99%

“…Nativestate landscape of ubiquitin has been explored both by experimental as well as computational means, [31][32][33] but only a few such reports are available in case of SUMO proteins. 30,[34][35][36] A flexible native-state can be crucial for functionality of proteins, 37,38 especially in cases where a single protein tackles multiple substrates single handedly, for example, SUMO protein in drosophila. 4 Conformational flexibility in any protein emanates from its excursion to low energy excited states, also called "near-native states," where its structure is slightly different from that of the native state.…”

mentioning

confidence: 99%

NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3)

et al. 2019

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Structural heterogeneity in the native‐state ensemble of dSmt3, the only small ubiquitin‐like modifier (SUMO) in Drosophila melanogaster, was investigated and compared with its human homologue SUMO1. Temperature dependence of amide proton's chemical shift was studied to identify amino acids possessing alternative structural conformations in the native state. Effect of small concentration of denaturant (1M urea) on this population was also monitored to assess the ruggedness of near‐native energy landscape. Owing to presence of many such amino acids, especially in the β2‐loop‐α region, the native state of dSmt3 seems more flexible in comparison to SUMO1. Information about backbone dynamics in ns‐ps timescale was quantified from the measurement of 15N‐relaxation experiments. Furthermore, the noncovalent interaction of dSmt3 and SUMO1 with Daxx12 (Daxx729DPEEIIVLSDSD740), a [V/I]‐X‐[V/I]‐[V/I]‐based SUMO interaction motif, was characterized using Bio‐layer Interferometery and NMR spectroscopy. Daxx12 fits itself in the groove formed by β2‐loop‐α structural region in both dSmt3 and SUMO1, but the binding is stronger with the former. Flexibility of β2‐loop‐α region in dSmt3 is suspected to assist its interaction with Daxx12. Our results highlight the role of native‐state flexibility in assisting noncovalent interactions of SUMO proteins especially in organisms where a single SUMO isoform has to tackle multiple substrates single handedly.

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Structural and functional analysis of SMO-1, the SUMO homolog in Caenorhabditis elegans

Cited by 10 publications

References 56 publications

SUMOylation of the chromodomain factor MRG-1 inC. elegansaffects chromatin-regulatory dynamics

SUMOylation of the chromodomain factor MRG-1 inC. elegansaffects chromatin-regulatory dynamics

Organism dual RNA‐seq reveals the importance of BarA/UvrY inVibrio parahaemolyticusvirulence

NMR characterization of conformational fluctuations and noncovalent interactions of SUMO protein from Drosophila melanogaster (dSmt3)

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