Solution structure of the RNA-binding cold-shock domain of the Chlamydomonas reinhardtii NAB1 protein and insights into RNA recognition

2015 ◽  
Vol 469 (1) ◽  
pp. 97-106 ◽  
Author(s):  
Anne L. Sawyer ◽  
Michael J. Landsberg ◽  
Ian L. Ross ◽  
Olaf Kruse ◽  
Mehdi Mobli ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Solution Structure ◽  
Cold Shock ◽  
Rna Binding ◽  
Specific Binding ◽  
Consensus Sequence ◽  
Rna Recognition ◽  
Nucleic Acid Binding ◽  
Cold Shock Domain ◽  
Higher Eukaryotes

We present the solution structure of the Chlamydomonas reinhardtii nucleic acid-binding protein 1 (NAB1) cold-shock domain (CSD) and compare this to homologues from bacteria and higher eukaryotes. Sequence-specific binding of the CSD consensus sequence (CSDCS) RNA element is also investigated.

scholarly journals Cold-Shock Domains—Abundance, Structure, Properties, and Nucleic-Acid Binding

Cancers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 190
Author(s):  
Udo Heinemann ◽  
Yvette Roske
Keyword(s):  
Cold Shock ◽  
Rna Binding ◽  
Binding Mode ◽  
Nucleic Acid Binding ◽  
Cold Shock Proteins ◽  
Dna And Rna ◽  
Promiscuous Dna ◽  
Human Proteins ◽  
Cold Shock Domain ◽  
Shock Proteins

The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.

scholarly journals Lin28, a major translation reprogramming factor, gains access to YB-1-packaged mRNA through its cold-shock domain

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anastasiia Samsonova ◽  
Krystel El Hage ◽  
Bénédicte Desforges ◽  
Vandana Joshi ◽  
Marie-Jeanne Clément ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Cold Shock ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Large Set ◽  
Core Component ◽  
The Core ◽  
Cold Shock Domain ◽  
Global Translation

AbstractThe RNA-binding protein Lin28 (Lin28a) is an important pluripotency factor that reprograms translation and promotes cancer progression. Although Lin28 blocks let-7 microRNA maturation, Lin28 also binds to a large set of cytoplasmic mRNAs directly. However, how Lin28 regulates the processing of many mRNAs to reprogram global translation remains unknown. We show here, using a structural and cellular approach, a mixing of Lin28 with YB-1 (YBX1) in the presence of mRNA owing to their cold-shock domain, a conserved β-barrel structure that binds to ssRNA cooperatively. In contrast, the other RNA binding-proteins without cold-shock domains tested, HuR, G3BP-1, FUS and LARP-6, did not mix with YB-1. Given that YB-1 is the core component of dormant mRNPs, a model in which Lin28 gains access to mRNPs through its co-association with YB-1 to mRNA may provide a means for Lin28 to reprogram translation. We anticipate that the translational plasticity provided by mRNPs may contribute to Lin28 functions in development and adaptation of cancer cells to an adverse environment.

scholarly journals Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis

2017 ◽  
Author(s):  
Kat S Moore ◽  
Nurcan Yagci ◽  
Floris van Alphen ◽  
Nahuel A Paolini ◽  
Rastislav Horos ◽  
...  
Keyword(s):  
Protein Expression ◽  
Mrna Expression ◽  
Mrna Stability ◽  
Cold Shock ◽  
Rna Binding ◽  
Mrna Translation ◽  
Mitochondrial Respiratory Chain ◽  
Protein Homeostasis ◽  
Diamond Blackfan Anemia ◽  
Cold Shock Domain

AbstractExpression of the RNA-binding protein Csde1 (Cold shock domain protein e1) is strongly upregulated during erythropoiesis compared to other hematopoietic lineages. In the severe congenital anemia Diamond Blackfan Anemia (DBA), however, Csde1 expression is impaired. Reduced expression of Csde1 in healthy erythroblasts impaired their proliferation and differentiation, which suggests an important role for Csde1 in erythropoiesis. To investigate the cellular pathways controlled by Csde1 in erythropoiesis, we identified the transcripts that physically associate with Csde1 in erythroid cells. These mainly encoded proteins involved in ribogenesis, mRNA translation and protein degradation, but also proteins associated with the mitochondrial respiratory chain and mitosis. Crispr/Cas9-mediated deletion of the first cold shock domain of Csde1 affected RNA expression and/or protein expression of Csde1-bound transcripts. For instance, protein expression of Pabpc1 was enhanced while Pabpc1 mRNA expression was reduced indicating more efficient translation of Pabpc1 followed by negative feedback on mRNA stability. Overall, the effect of reduced Csde1 function on mRNA stability and translation of Csde1-bound transcripts was modest. Clones with complete loss of Csde1, however, could not be generated. We suggest that Csde1 is involved in feed-back control in protein homeostasis and that it dampens stochastic changes in mRNA expression.

piRNAs Interact with Cold-Shock Domain-Containing RNA Binding Proteins and Regulate Neuronal Gene Expression During Differentiation

2022 ◽  
Author(s):  
Charannya Sozheesvari Subhramanyam ◽  
Qiong Cao ◽  
Cheng Wang ◽  
Zealyn Shi-Lin Heng ◽  
Zhihong Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Proteins ◽  
Cold Shock ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neuronal Gene ◽  
Cold Shock Domain

scholarly journals Ribonucleocapsid Formation of Severe Acute Respiratory Syndrome Coronavirus through Molecular Action of the N-Terminal Domain of N Protein

2007 ◽  
Vol 81 (8) ◽  
pp. 3913-3921 ◽  
Author(s):  
Kumar Singh Saikatendu ◽  
Jeremiah S. Joseph ◽  
Vanitha Subramanian ◽  
Benjamin W. Neuman ◽  
Michael J. Buchmeier ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Solution Structure ◽  
Rna Binding ◽  
Crystal Packing ◽  
Rna Recognition ◽  
Viral Membrane ◽  
Ribonucleoprotein Complex ◽  
N Protein ◽  
Cubic Form ◽  
Terminal Domain

ABSTRACT Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 Å (monoclinic) and at 1.85 Å (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the β-sheet core. The functionally important positively charged β-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

scholarly journals A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ

2019 ◽  
Vol 75 (6) ◽  
pp. 439-449 ◽  
Author(s):  
Thushara Welwelwela Hewage ◽  
Sofia Caria ◽  
Mihwa Lee
Keyword(s):  
Crystal Structure ◽  
Small Angle ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Protein ◽  
Coiled Coil ◽  
Scattering Data ◽  
Nucleic Acid Binding ◽  
Dimerization Domain ◽  
Orthorhombic Space Group

Splicing factor proline/glutamine-rich (SFPQ) is an essential RNA-binding protein that is implicated in many aspects of nuclear function. The structures of SFPQ and two paralogs, non-POU domain-containing octamer-binding protein and paraspeckle component 1, from theDrosophilabehavior human splicing protein family have previously been characterized. The unusual arrangement of the four domains, two RNA-recognition motifs (RRMs), a conserved region termed the NonA/paraspeckle (NOPS) domain and a C-terminal coiled coil, in the intertwined dimer provides a potentially unique RNA-binding surface. However, the molecular details of how the four RRMs in the dimeric SFPQ interact with RNA remain to be characterized. Here, a new crystal structure of the dimerization domain of human SFPQ in theC-centered orthorhombic space groupC2221with one monomer in the asymmetric unit is presented. Comparison of the new crystal structure with the previously reported structure of SFPQ and analysis of the solution small-angle X-scattering data revealed subtle domain movements in the dimerization domain of SFPQ, supporting the concept of multiple conformations of SFPQ in equilibrium in solution. The domain movement of RRM1, in particular, may reflect the complexity of the RNA substrates of SFPQ. Taken together, the crystal and solution structure analyses provide a molecular basis for further investigation into the plasticity of nucleic acid binding by SFPQ in the absence of the structure in complex with its cognate RNA-binding partners.

scholarly journals Direct, sequence-specific binding of the human U1-70K ribonucleoprotein antigen protein to loop I of U1 small nuclear RNA.

1989 ◽  
Vol 9 (10) ◽  
pp. 4179-4186 ◽  
Author(s):  
C S Surowy ◽  
V L van Santen ◽  
S M Scheib-Wixted ◽  
R A Spritz
Keyword(s):  
Fusion Protein ◽  
Rna Binding ◽  
Specific Binding ◽  
Consensus Sequence ◽  
Small Nuclear Rna ◽  
Small Nuclear Ribonucleoprotein ◽  
U1 Snrna ◽  
Nuclear Rna ◽  
Mutation Analyses

We have studied the interaction of two of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins, U1-70K and U1-A, with U1 small nuclear RNA (snRNA). The U1-70K protein is a U1-specific RNA-binding protein. Deletion and mutation analyses of a beta-galactosidase/U1-70K partial fusion protein indicated that the central portion of the protein, including the RNP sequence domain, is both necessary and sufficient for specific U1 snRNA binding in vitro. The highly conserved eight-amino-acid RNP consensus sequence was found to be essential for binding. Deletion and mutation analyses of U1 snRNA showed that both the U1-70K fusion protein and the native HeLa U1-70K protein bound directly to loop I of U1 snRNA. Binding was sequence specific, requiring 8 of the 10 bases in the loop. The U1-A snRNP protein also interacted specifically with U1 snRNA, principally with stem-loop II.

scholarly journals The design and structural characterization of a synthetic pentatricopeptide repeat protein

2015 ◽  
Vol 71 (2) ◽  
pp. 196-208 ◽  
Author(s):  
Benjamin S. Gully ◽  
Kunal R. Shah ◽  
Mihwa Lee ◽  
Kate Shearston ◽  
Nicole M. Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Proteins ◽  
Rna Binding ◽  
De Novo ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Consensus Sequence ◽  
Pentatricopeptide Repeat ◽  
Ppr Protein ◽  
Ppr Proteins

Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to thede novodesign of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.

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