scholarly journals Deconstructing the structural conservation of distantly related bacterial nucleoid-associated proteins using functional chimeras

2019 ◽  
Author(s):  
Rogério F. Lourenço ◽  
Saumya Saurabh ◽  
Jonathan Herrmann ◽  
Soichi Wakatsuki ◽  
Lucy Shapiro
Keyword(s):  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Structural Elements ◽  
Phylogenetic Groups ◽  
Sequence Element ◽  
Force Microscopy ◽  
Associated Proteins ◽  
Self Association ◽  
And Function

ABSTRACTNucleoid-associated proteins (NAPs) are DNA-binding proteins critical for the organization and function of the bacterial chromosome. A subclass of NAPs, including Caulobacter crescentus GapR and Escherichia coli H-NS, preferentially bind AT-rich regions of the nucleoid, but phylogenetic groups that encode GapR rarely encode H-NS. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recent DNA-bound crystal structure of GapR (Guo et al, 2018), we show that although evolutionarily distant, GapR and H-NS possess two regions that are structurally and functionally conserved. These regions are involved in self-association and DNA-binding, even though the two proteins oligomerize and regulate transcription differently. Functional analysis of GapR and H-NS protein chimeras identified structural elements present in H-NS but absent in GapR that rationalize differences in transcriptional regulation. In addition, we identified a sequence element unique to GapR that enables assembly into its tetrameric state. Using fluid-atomic force microscopy, we showed that GapR is capable of bridging DNA molecules in vitro. Together, these results demonstrate that two distantly related NAPs utilize evolutionarily conserved structural elements to serve specialized cellular roles via distinct mechanisms.

scholarly journals The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Rogério F. Lourenço ◽  
Saumya Saurabh ◽  
Jonathan Herrmann ◽  
Soichi Wakatsuki ◽  
Lucy Shapiro
Keyword(s):  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Genetic Material ◽  
Bacterial Cells ◽  
Structural Elements ◽  
Content Type ◽  
Time Dynamic ◽  
Associated Proteins ◽  
And Function

ABSTRACT Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA. IMPORTANCE Bacteria organize their genetic material in a structure called the nucleoid, which needs to be compact to fit inside the cell and, at the same time, dynamic to allow high rates of replication and transcription. Nucleoid-associated proteins (NAPs) play a pivotal role in this process, so their detailed characterization is crucial for our understanding of DNA organization into bacterial cells. Even though NAPs affect DNA-related processes differently, all of them have to oligomerize and bind DNA for their function. The significance of this study is the identification of structural elements involved in the oligomerization and DNA binding of a newly discovered NAP in C. crescentus and the demonstration that structural elements are conserved in evolutionarily distant and functionally distinct NAPs.

Structure and function of bacterial H-NS protein

2016 ◽  
Vol 44 (6) ◽  
pp. 1561-1569 ◽  
Author(s):  
David C. Grainger
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Genome Evolution ◽  
Protein A ◽  
Structure And Function ◽  
Dna Condensation ◽  
Structural Elements ◽  
Small Peptide ◽  
Self Association ◽  
And Function

The histone-like nucleoid structuring (H-NS) protein is a major component of the folded chromosome in Escherichia coli and related bacteria. Functions attributed to H-NS include management of genome evolution, DNA condensation, and transcription. The wide-ranging influence of H-NS is remarkable given the simplicity of the protein, a small peptide, possessing rudimentary determinants for self-association, hetero-oligomerisation and DNA binding. In this review, I will discuss our understanding of H-NS with a focus on these structural elements. In particular, I will consider how these interaction surfaces allow H-NS to exert its different effects.

Molecular architecture and functions of the neuronal cytoskeleton

1990 ◽  
Vol 48 (3) ◽  
pp. 2-3
Author(s):  
Nobutaka Hirokawa
Keyword(s):  
Major Elements ◽  
Molecular Structures ◽  
Organelle Transport ◽  
Molecular Architecture ◽  
Neuronal Morphogenesis ◽  
Microtubule Associated Proteins ◽  
Associated Proteins ◽  
And Function ◽  
Small Clusters

In this symposium I will present our studies about the molecular architecture and function of the cytomatrix of the nerve cells. The nerve cell is a highly polarized cell composed of highly branched dendrites, cell body, and a single long axon along the direction of the impulse propagation. Each part of the neuron takes characteristic shapes for which the cytoskeleton provides the framework. The neuronal cytoskeletons play important roles on neuronal morphogenesis, organelle transport and the synaptic transmission. In the axon neurofilaments (NF) form dense arrays, while microtubules (MT) are arranged as small clusters among the NFs. On the other hand, MTs are distributed uniformly, whereas NFs tend to run solitarily or form small fascicles in the dendrites Quick freeze deep etch electron microscopy revealed various kinds of strands among MTs, NFs and membranous organelles (MO). These structures form major elements of the cytomatrix in the neuron. To investigate molecular nature and function of these filaments first we studied molecular structures of microtubule associated proteins (MAP1A, MAP1B, MAP2, MAP2C and tau), and microtubules reconstituted from MAPs and tubulin in vitro. These MAPs were all fibrous molecules with different length and formed arm like projections from the microtubule surface.

scholarly journals Membrane-associated phase separation: organization and function emerge from a two-dimensional milieu

2021 ◽  
Author(s):  
Jonathon A Ditlev
Keyword(s):  
Phase Separation ◽  
Cell Biology ◽  
Cellular Environment ◽  
Condensate Formation ◽  
Associated Proteins ◽  
Available Technology ◽  
And Function ◽  
Surrounding Membrane

Abstract Liquid‒liquid phase separation (LLPS) of biomolecules has emerged as an important mechanism that contributes to cellular organization. Phase separated biomolecular condensates, or membrane-less organelles, are compartments composed of specific biomolecules without a surrounding membrane in the nucleus and cytoplasm. LLPS also occurs at membranes, where both lipids and membrane-associated proteins can de-mix to form phase separated compartments. Investigation of these membrane-associated condensates using in vitro biochemical reconstitution and cell biology has provided key insights into the role of phase separation in membrane domain formation and function. However, these studies have generally been limited by available technology to study LLPS on model membranes and the complex cellular environment that regulates condensate formation, composition, and function. Here, I briefly review our current understanding of membrane-associated condensates, establish why LLPS can be advantageous for certain membrane-associated condensates, and offer a perspective for how these condensates may be studied in the future.

scholarly journals DNA-Binding Properties of YbaB, a Putative Nucleoid-Associated Protein From Caulobacter crescentus

2021 ◽  
Vol 12 ◽  
Author(s):  
Parul Pal ◽  
Malvika Modi ◽  
Shashank Ravichandran ◽  
Ragothaman M. Yennamalli ◽  
Richa Priyadarshini
Keyword(s):  
Gene Regulation ◽  
Dna Binding ◽  
Caulobacter Crescentus ◽  
Binding Protein ◽  
Bacterial Species ◽  
Physiological Role ◽  
Dna Binding Protein ◽  
Associated Proteins ◽  
Family Gene ◽  
Almost All

Nucleoid-associated proteins (NAPs) or histone-like proteins (HLPs) are DNA-binding proteins present in bacteria that play an important role in nucleoid architecture and gene regulation. NAPs affect bacterial nucleoid organization via DNA bending, bridging, or forming aggregates. EbfC is a nucleoid-associated protein identified first in Borrelia burgdorferi, belonging to YbaB/EbfC family of NAPs capable of binding and altering DNA conformation. YbaB, an ortholog of EbfC found in Escherichia coli and Haemophilus influenzae, also acts as a transcriptional regulator. YbaB has a novel tweezer-like structure and binds DNA as homodimers. The homologs of YbaB are found in almost all bacterial species, suggesting a conserved function, yet the physiological role of YbaB protein in many bacteria is not well understood. In this study, we characterized the YbaB/EbfC family DNA-binding protein in Caulobacter crescentus. C. crescentus has one YbaB/EbfC family gene annotated in the genome (YbaBCc) and it shares 41% sequence identity with YbaB/EbfC family NAPs. Computational modeling revealed tweezer-like structure of YbaBCc, a characteristic of YbaB/EbfC family of NAPs. N-terminal–CFP tagged YbaBCc localized with the nucleoid and is able to compact DNA. Unlike B. burgdorferi EbfC protein, YbaBCc protein is a non-specific DNA-binding protein in C. crescentus. Moreover, YbaBCc shields DNA against enzymatic degradation. Collectively, our findings reveal that YbaBCc is a small histone-like protein and may play a role in bacterial chromosome structuring and gene regulation in C. crescentus.

scholarly journals Residue R113 Is Essential for PhoP Dimerization and Function: a Residue Buried in the Asymmetric PhoP Dimer Interface Determined in the PhoPN Three-Dimensional Crystal Structure

2003 ◽  
Vol 185 (1) ◽  
pp. 262-273 ◽  
Author(s):  
Yinghua Chen ◽  
Catherine Birck ◽  
Jean-Pierre Samama ◽  
F. Marion Hulett
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Salt Bridge ◽  
Pho Regulon ◽  
Dimer Interface ◽  
And Function ◽  
Negative Phenotype

ABSTRACT Bacillus subtilis PhoP is a member of the OmpR/PhoB family of response regulators that is directly required for transcriptional activation or repression of Pho regulon genes in conditions under which Pi is growth limiting. Characterization of the PhoP protein has established that phosphorylation of the protein is not essential for PhoP dimerization or DNA binding but is essential for transcriptional regulation of Pho regulon genes. DNA footprinting studies of PhoP-regulated promoters showed that there was cooperative binding between PhoP dimers at PhoP-activated promoters and/or extensive PhoP oligomerization 3′ of PhoP-binding consensus repeats in PhoP-repressed promoters. The crystal structure of PhoPN described in the accompanying paper revealed that the dimer interface between two PhoP monomers involves nonidentical surfaces such that each monomer in a dimer retains a second surface that is available for further oligomerization. A salt bridge between R113 on one monomer and D60 on another monomer was judged to be of major importance in the protein-protein interaction. We describe the consequences of mutation of the PhoP R113 codon to a glutamate or alanine codon and mutation of the PhoP D60 codon to a lysine codon. In vivo expression of either PhoPR113E, PhoPR113A, or PhoPD60K resulted in a Pho-negative phenotype. In vitro analysis showed that PhoPR113E was phosphorylated by PhoR (the cognate histidine kinase) but was unable to dimerize. Monomeric PhoPR113E∼P was deficient in DNA binding, contributing to the PhoPR113E in vivo Pho-negative phenotype. While previous studies emphasized that phosphorylation was essential for PhoP function, data reported here indicate that phosphorylation is not sufficient as PhoP dimerization or oligomerization is also essential. Our data support the physiological relevance of the residues of the asymmetric dimer interface in PhoP dimerization and function.

scholarly journals The nucleoid-associated protein Gbn binds to GATC sequences and affects sporulation and antibiotic production in Streptomyces

2021 ◽  
Author(s):  
Chao Du ◽  
Joost Willemse ◽  
Amanda M. Erkelens ◽  
Victor J. Carrion ◽  
Remus T. Dame ◽  
...  
Keyword(s):  
Dna Binding ◽  
Chromatin Immunoprecipitation ◽  
Antibiotic Production ◽  
Consensus Sequence ◽  
Associated Proteins ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Number Of Binding Sites ◽  
Trna Editing ◽  
Editing Enzyme

ABSTRACTBacterial chromosome structure is organized by a diverse group of proteins collectively called nucleoid-associated proteins (NAPs). Many NAPs have been studied in detail in Streptomyces, including Lsr2, HupA, HupS, and sIHF. Here, we show that SCO1839 represents a novel family of small NAPs unique to Actinobacteria and recognizes a consensus sequence consisting of GATC followed by (A/T)T. The protein was designated Gbn for GATC-binding NAP. Chromatin immunoprecipitation sequencing (ChIP-Seq) detected more than 2800 binding regions, encompassing some 3600 GATCWT motifs, which comprise 55% of all motifs in the S. coelicolor genome. DNA binding of Gbn in vitro increased DNA stiffness but not compaction, suggesting a role in regulation rather than chromosome organization. Despite the huge number of binding sites, the DNA binding profiles were nearly identical during vegetative and aerial growth. The exceptions were SCO1311 and SCOt32, for a tRNA editing enzyme and a tRNA that recognises the rare leucine codon CUA, respectively, which were nearly exclusively bound during vegetative growth. Deletion of gbn led to pleiotropic alterations in developmental timing, morphogenesis and antibiotic production. Taken together, our data show that Gbn is a highly pleiotropic NAP that impacts growth and development in streptomycetes.

scholarly journals Study of the structure and function of the HURP protein during mitotic division

2013 ◽  
Author(s):  
Κωνσταντίνος Νάκος
Keyword(s):  
Dna Binding ◽  
Xenopus Laevis ◽  
Histone Deacetylase ◽  
Dna Binding Protein ◽  
Mitotic Division ◽  
Structure And Function ◽  
Aurora A ◽  
Nucleosome Remodeling ◽  
And Function

Η πρωτεΐνη HURP (Hepatoma Up-Regulated protein) έχει αναγνωριστεί ως παράγονταςσυναρμολόγησης της ατράκτου (SAF) που ρυθμίζεται από τη RanGTP. Αρχικά βρέθηκε σε μιτωτικάεκχυλίσματα αυγών Xenopus laevis, σε σύμπλοκο με τις TPX2, XMAP215, Eg5 και Aurora A. Η HURPπροσδένεται στους μικροσωληνίσκους, εντοπίζεται κυρίως στους μικροσωληνίσκους των κινητοχώρωνκαι είναι απαραίτητη για την σωστή συναρμολόγηση της μιτωτικής ατράκτου. Παρόλο αυτά, πρωτεΐνεςπου αλληλεπιδρούν με τη HURP σε ανθρώπινα κύτταρα παραμένουν άγνωστες.Σε αυτή τη μελέτη περιγράφουμε την αναγνώριση μίας νέας πρωτεΐνης που αλληλεπιδρά με τη HURP,τη CHD4 (Chromodomain Helicase DNA binding protein 4) μία ATPάση της αναδιαμόρφωσης τηςχρωματίνης και καταλυτική υπομονάδα του συμπλόκου αποκετυλασών που ευθύνεται για τηναναδιαμόρφωση του νουκλεοσώματος (Nucleosome remodeling and histone Deacetylase - NuRD).Πρόσφατα η πρωτεΐνη CHD4 αναγνωρίστηκε ως πρωτεΐνη που προσδένεται στους μικροσωληνίσκουςκαι ρυθμίζεται από την RanGTP.Οι μελέτες μας σε ανθρώπινα κύτταρα έδειξαν ότι η CHD4 κατά τη μίτωση απελευθερώνεται από ταμιτωτικά χρωμοσώματα και εντοπίζεται στην άτρακτο, υποδεικνύοντας ένα καινούριο ρόλο της CHD4στη συναρμολόγηση της ατράκτου. Για να κατανοήσουμε τη λειτουργία της CHD4 πραγματοποιήσαμεμελέτες απαλοιφής της CHD4 με την τεχνική της αποσιώπισης γονιδίου με siRNA. Μείωση της CHD4προκαλεί βλάβες στη συναρμολόγηση της μιτωτικής ατράκτου και στη στοίχιση των χρωμοσωμάτωνστις αρχές της μίτωσης, οδηγώντας σε ανώμαλο διαχωρισμό των χρωμοσωμάτων. Επιπλέον, ηαπώλεια της CHD4 επηρρεάζει τη σταθερότητα των K-fibers μειώνοντας σημαντικά την ποσότητα των μικροσωληνίσκων των κινητοχώρων. Μετά την απαλοιφή της CHD4, ο εντοπισμός της HURP βρέθηκενα αλλάζει, χάνοντας την προτίμησή της για τους μικροσωληνίσκους, των κινητοχώρων,υποδεικνύοντας την πιθανή ρύθμιση του εντοπισμού της HURP από την CHD4. Τέλος από in vitro καιin vivo πειράματα, βρήκαμε ότι η CHD4 αλληλεπιδρά με τη μιτωτική κινάση Aurora A και την πρωτεΐνηTPX2 που συνδέεται με μικροσωληνίσκους, δημιουργώντας ένα καινούριο σύμπλοκο σημαντικό για τηλειτουργία της μιτωτικής ατράκτου στα κύτταρα θηλαστικών.

Self-Association Contributes to E2a-Pbx1-Mediated Oncogenesis.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2611-2611
Author(s):  
Zhong Wang ◽  
Michael L. Cleary
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Nuclear Localization ◽  
Chromosomal Translocations ◽  
Bhlh Protein ◽  
Alternative Mechanism ◽  
Homeodomain Proteins ◽  
Oncogenic Activity ◽  
Self Association

Abstract Pbx1 is a proto-oncogene that was originally discovered at the site of t(1;19) chromosomal translocations in pediatric acute B cell precursor leukemia. It codes for a TALE (three amino acid loop extension) class homeodomain transcription factor, which is a component of hetero-oligomeric protein complexes that regulate developmental gene expression. As a result of chromosomal translocations, Pbx1 is oncogenically activated by in-frame fusions with the E2a bHLH protein, which confers strong transcriptional activator properties and constitutive nuclear localization, bypassing the need for dimerization with Meinox homeodomain proteins to stabilize and import Pbx1 into the nucleus. E2a-Pbx1 oncoproteins retain an ability to bind DNA as a complex with Hox transcription factors, and co-expressed HoxA9 accelerates leukemogenesis. Using a biochemical approach, we have recently observed that E2a-Pbx1 self-associates through the Pbx moiety of the chimeric protein to form higher-order oligomers. Structure/function studies suggest that self-association is required for oncogenic activity since mutant E2a-Pbx1 proteins unable to self-associate are transformation defective in an in vitro myeloid progenitor serial replating assay. Interestingly, their oncogenic activity in this assay is rescued using synthetic oligomerization domains of FKBP. The drug AP21998, which disrupts FKBP-mediated oligomerization, blocks the proliferation of transformed myeloid progenitors and facilitates their terminal myeloid differentiation. In addition to self-association, the DNA binding homeodomain of Pbx1 is also required for transformation, but mutagenesis studies indicate that Pbx1 domains involved in cooperative DNA binding with Hox partners are dispensable. These studies suggest an alternative mechanism for leukemogenesis in which E2a-Pbx1 deregulates subordinate gene expression as an oligomeric complex that circumvents interactions with heterologous homeodomain proteins that otherwise modulate Pbx1 nuclear localization, DNA binding, and transcriptional activity.

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