Structure, Activity, and Function of SETMAR Protein Lysine Methyltransferase

SETMAR is a protein lysine methyltransferase that is involved in several DNA processes, including DNA repair via the non-homologous end joining (NHEJ) pathway, regulation of gene expression, illegitimate DNA integration, and DNA decatenation. However, SETMAR is an atypical protein lysine methyltransferase since in anthropoid primates, the SET domain is fused to an inactive DNA transposase. The presence of the DNA transposase domain confers to SETMAR a DNA binding activity towards the remnants of its transposable element, which has resulted in the emergence of a gene regulatory function. Both the SET and the DNA transposase domains are involved in the different cellular roles of SETMAR, indicating the presence of novel and specific functions in anthropoid primates. In addition, SETMAR is dysregulated in different types of cancer, indicating a potential pathological role. While some light has been shed on SETMAR functions, more research and new tools are needed to better understand the cellular activities of SETMAR and to investigate the therapeutic potential of SETMAR.

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Structure, Activity, and Function of SETMAR protein Lysine Methyltransferase

10.20944/preprints202111.0164.v1 ◽

2021 ◽

Author(s):

Michael Tellier

Keyword(s):

Therapeutic Potential ◽

Regulation Of Gene Expression ◽

Binding Activity ◽

Regulatory Function ◽

Dna Binding Activity ◽

Lysine Methyltransferase ◽

Anthropoid Primates ◽

Pathway Regulation ◽

Non Homologous End Joining ◽

And Function

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The Drosophila extramacrochaetae protein antagonizes sequence-specific DNA binding by daughterless/achaete-scute protein complexes

Development ◽

10.1242/dev.113.1.245 ◽

1991 ◽

Vol 113 (1) ◽

pp. 245-255 ◽

Cited By ~ 32

Author(s):

M. Van Doren ◽

H.M. Ellis ◽

J.W. Posakony

Keyword(s):

Dna Binding ◽

Cell Fate ◽

Protein Complexes ◽

Competitive Inhibitor ◽

Binding Activity ◽

Regulatory Function ◽

Biochemical Basis ◽

Dna Binding Activity

In Drosophila, a group of regulatory proteins of the helix-loop-helix (HLH) class play an essential role in conferring upon cells in the developing adult epidermis the competence to give rise to sensory organs. Proteins encoded by the daughterless (da) gene and three genes of the achaete-scute complex (AS-C) act positively in the determination of the sensory organ precursor cell fate, while the extramacrochaetae (emc) and hairy (h) gene products act as negative regulators. In the region upstream of the achaete gene of the AS-C, we have identified three ‘E box’ consensus sequences that are bound specifically in vitro by hetero-oligomeric complexes consisting of the da protein and an AS-C protein. We have used this DNA-binding activity to investigate the biochemical basis of the negative regulatory function of emc. Under the conditions of our experiments, the emc protein, but not the h protein, is able to antagonize specifically the in vitro DNA-binding activity of da/AS-C and putative da/da protein complexes. We interpret these results as follows: the heterodimerization capacity of the emc protein (conferred by its HLH domain) allows it to act in vivo as a competitive inhibitor of the formation of functional DNA-binding protein complexes by the da and AS-C proteins, thereby reducing the effective level of their transcriptional regulatory activity within the cell.

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Regulation of Transcription Factors and Repression of Sp1 by Prolactin Signaling Through the Short Isoform of Its Cognate Receptor

Endocrinology ◽

10.1210/en.2008-1719 ◽

2009 ◽

Vol 150 (7) ◽

pp. 3327-3335 ◽

Cited By ~ 20

Author(s):

Y. Sangeeta Devi ◽

Aurora Shehu ◽

Carlos Stocco ◽

Julia Halperin ◽

Jamie Le ◽

...

Keyword(s):

Transcription Factors ◽

Signaling Pathway ◽

Short Form ◽

Binding Activity ◽

In Vivo Model ◽

Regulation Of Transcription ◽

Signaling Mechanism ◽

Dna Binding Activity ◽

And Function

Prolactin (PRL) affects the development and function of the reproductive system by binding to two types of receptors, which differ by the size of their intracellular domain in rodents. Whereas the signaling pathway through the long form of the receptor (PRL-RL) is well characterized, signaling through the short form (PRL-RS) remains obscure. In this investigation, we examined transcription factors regulated by PRL in the ovary and decidua of mice expressing only PRL-RS in a PRL receptor null background. These mice provide a powerful in vivo model to study the selective signaling mechanism of PRL through PRL-RS independent of PRL-RL. We also examined the regulation of transcription factors in ovarian and uterine cell lines stably transfected with PRL-RS or PRL-RL. We focused our investigation on transcription factors similarly regulated in both these tissues and clearly established that signaling through PRL-RS does not activate the JaK/Stat in vivo but leads to severe down-regulation of Sp1 expression, DNA binding activity, and nuclear localization, events that appear to involve the calmodulin-dependent protein kinase pathway. Our in vivo and in culture data demonstrate that the PRL-RS activates a signaling pathway distinct from that of the PRL-RL.

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Inhibition of DNA Binding by Differential Sumoylation of Heat Shock Factors

Molecular and Cellular Biology ◽

10.1128/mcb.26.3.955-964.2006 ◽

2006 ◽

Vol 26 (3) ◽

pp. 955-964 ◽

Cited By ~ 74

Author(s):

Julius Anckar ◽

Ville Hietakangas ◽

Konstantin Denessiouk ◽

Dennis J. Thiele ◽

Mark S. Johnson ◽

...

Keyword(s):

Heat Shock ◽

Dna Binding ◽

Regulation Of Gene Expression ◽

Binding Activity ◽

Covalent Modification ◽

Heat Shock Factors ◽

Substrate Selection ◽

Binding Domains ◽

Dna Binding Activity ◽

Specific Regulation

ABSTRACT Covalent modification of proteins by the small ubiquitin-related modifier SUMO regulates diverse biological functions. Sumoylation usually requires a consensus tetrapeptide, through which the binding of the SUMO-conjugating enzyme Ubc9 to the target protein is directed. However, additional specificity determinants are in many cases required. To gain insights into SUMO substrate selection, we have utilized the differential sumoylation of highly similar loop structures within the DNA-binding domains of heat shock transcription factor 1 (HSF1) and HSF2. Site-specific mutagenesis in combination with molecular modeling revealed that the sumoylation specificity is determined by several amino acids near the consensus site, which are likely to present the SUMO consensus motif to Ubc9. Importantly, we also demonstrate that sumoylation of the HSF2 loop impedes HSF2 DNA-binding activity, without affecting its oligomerization. Hence, SUMO modification of the HSF2 loop contributes to HSF-specific regulation of DNA binding and broadens the concept of sumoylation in the negative regulation of gene expression.

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The interaction of proteins encoded by Drosophila homeotic and segmentation genes with specific DNA sequences

Development ◽

10.1242/dev.104.supplement.75 ◽

1988 ◽

Vol 104 (Supplement) ◽

pp. 75-83 ◽

Cited By ~ 2

Author(s):

Allen Laughon ◽

William Howell ◽

Matthew P. Scott

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Binding Sites ◽

Binding Activity ◽

Regulatory Function ◽

Temperature Sensitive ◽

Structural Domain ◽

Dna Binding Activity ◽

Dna Restriction Fragments

The ANT-C gene cluster is part of a network of genes that govern pattern formation in the development of Drosophila. The ANT-C genes encode proteins that contain a conserved 60 amino acid sequence, the homeodomain. Here we show that the homeodomains encoded by two of the ANT-C loci confer sequencespecific DNA-binding activity. The DNA sequence specificities of the Dfd and ftz homeodomains appear to overlap completely in vitro, indicating that differences in regulatory specificity among ANT-C and BX-C proteins (assuming that differences exist) must be a consequence of the nonconserved protein sequences found outside of the homeodomains. Deletions that remove sequences from either end of the ftz homeodomain abolish DNA-binding activity, consistent with the commonly held assumption that the homeodomain is a structural domain. The relevance of in vitro DNA-binding experiments to the regulatory function of ftz is supported by our finding that a temperature-sensitive ftz mutation that causes a pairwise fusion of embryonic segments also reduces the affinity of the ftz homeodomain for DNA. Restriction fragments containing ftz homeodomain binding sites were identified within a 90 kb stretch of DNA extending the Antp P1 and P2 promoters. Binding sites appear to be clustered near the P1 promoter but also occur near P2 and in the region between the two. The task remains of determining which of these sequences mediate regulation of Antp by ftz or by other genes that encode closely related homeodomains.

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The Vitamin B 12 -Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

mBio ◽

10.1128/mbio.00261-17 ◽

2017 ◽

Vol 8 (2) ◽

Cited By ~ 4

Author(s):

Mingxu Fang ◽

Carl E. Bauer

Keyword(s):

Gene Expression ◽

Dna Binding ◽

Light Absorption ◽

Growth Conditions ◽

Binding Activity ◽

Regulatory Function ◽

Vitamin B ◽

Dna Binding Activity

ABSTRACT Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B 12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ 2 ) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ 2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. IMPORTANCE Photoreceptors control a wide range of physiology often by regulating downstream gene expression in response to light absorption via a bound chromophore. Different photoreceptors are known to utilize a number of different compounds for light absorption, including the use of such compounds as flavins, linearized tetrapyrroles (bilins), and carotenoids. Recently, a novel class of photoreceptors that use vitamin B 12 (cobalamin) as a blue-light-absorbing chromophore have been described. In this study, we analyzed the mechanism by which the vitamin B 12 binding photoreceptor AerR controls the DNA binding activity of the photosystem regulator CrtJ. This study shows that a direct interaction between the vitamin B 12 binding photoreceptor AerR with CrtJ modulates CrtJ binding to DNA and importantly, the regulatory outcome of gene expression, as shown here with photosystem promoters.

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The regulatory function of dIno80 correlates with its DNA binding activity

Gene ◽

10.1016/j.gene.2020.144368 ◽

2020 ◽

Vol 732 ◽

pp. 144368 ◽

Cited By ~ 1

Author(s):

Shruti Jain ◽

Jayant Maini ◽

Ankita Narang ◽

Souvik Maiti ◽

Vani Brahmachari

Keyword(s):

Dna Binding ◽

Binding Activity ◽

Regulatory Function ◽

Dna Binding Activity

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Phenotypic Analysis of Random hnsMutations Differentiate DNA-Binding Activity from Properties offimA Promoter Inversion Modulation and Bacterial Motility

Journal of Bacteriology ◽

10.1128/jb.181.3.941-948.1999 ◽

1999 ◽

Vol 181 (3) ◽

pp. 941-948 ◽

Cited By ~ 18

Author(s):

Gina M. Donato ◽

Thomas H. Kawula

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Constitutive Expression ◽

Binding Activity ◽

Single Amino Acid ◽

Amino Acid Substitutions ◽

Phenotypic Analysis ◽

Mutator Strain ◽

Dna Binding Activity ◽

And Function

ABSTRACT H-NS is a major Escherichia coli nucleoid-associated protein involved in bacterial DNA condensation and global modulation of gene expression. This protein exists in cells as at least two different isoforms separable by isoelectric focusing. Among other phenotypes, mutations in hns result in constitutive expression of theproU and fimB genes, increased fimApromoter inversion rates, and repression of the flhCDmaster operon required for flagellum biosynthesis. To understand the relationship between H-NS structure and function, we transformed a cloned hns gene into a mutator strain and collected a series of mutant alleles that failed to repress proUexpression. Each of these isolated hns mutant alleles also failed to repress fimB expression, suggesting that H-NS-specific repression of proU and fimBoccurs by similar mechanisms. Conversely, alleles encoding single amino acid substitutions in the C-terminal DNA-binding domain of H-NS resulted in significantly reduced affinity for DNA yet conferred a wild-type fimA promoter inversion frequency, indicating that the mechanism of H-NS activity in modulating promoter inversion is independent of DNA binding. Furthermore, two specific H-NS amino acid substitutions resulted in hypermotile bacteria, while C-terminal H-NS truncations exhibited reduced motility. We also analyzed H-NS isoform composition expressed by various hnsmutations and found that the N-terminal 67 amino acids were sufficient to support posttranslational modification and that substitutions at positions 18 and 26 resulted in the expression of a single H-NS isoform. These results are discussed in terms of H-NS domain organization and implications for biological activity.

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Stat4, a novel gamma interferon activation site-binding protein expressed in early myeloid differentiation.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4342 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4342-4349 ◽

Cited By ~ 137

Author(s):

K Yamamoto ◽

F W Quelle ◽

W E Thierfelder ◽

B L Kreider ◽

D J Gilbert ◽

...

Keyword(s):

Tyrosine Phosphorylation ◽

Regulation Of Gene Expression ◽

Myeloid Cells ◽

Binding Activity ◽

Gamma Interferon ◽

Chromosome 1 ◽

Ifn Gamma ◽

Dna Binding Activity ◽

Related Proteins ◽

Stimulating Factor

Interferon regulation of gene expression is dependent on the tyrosine phosphorylation and activation of the DNA-binding activity of two related proteins of 91 kDa (STAT1) and/or 113 kDa (STAT2). Recent studies have suggested that these proteins are substrates of Janus kinases and that proteins related in STAT1 are involved in a number of signalling pathways, including those activated in myeloid cells by erythropoietin and interleukin-3 (IL-3). To clone STAT-related proteins from myeloid cells, degenerate oligonucleotides were used in PCRs to identify novel family members expressed in myeloid cells. This approach allowed the identification and cloning of the Stat4 gene, which is 52% identical to STAT1. Unlike STAT1, Stat4 expression is restricted but includes myeloid cells and spermatogonia. In the erythroid lineage, Stat4 expression is differentially regulated during differentiation. Functionally, Stat4 has the properties of other STAT family genes. In particular, cotransfection of expression constructs for Stat4 and Jak1 and Jak2 results in the tyrosine phosphorylation of Stat4 and the acquisition of the ability to bind to the gamma interferon (IFN-gamma)-activated sequence of the interferon regulatory factor 1 (IRF-1) gene. Stat4 is located on mouse chromosome 1 and is tightly linked to the Stat1 gene, suggesting that the genes arose by gene duplication. Unlike Stat1, neither IFN-alpha nor IFN-gamma activates Stat4. Nor is Stat4 activated in myeloid cells by a number of cytokines, including erythropoietin, IL-3, granulocyte colony-stimulating factor, stem cell factor, colon-stimulating factor 1, hepatocyte growth factor, IL-2, IL-4, and IL-6.

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Role and Function of Class III LitR, a Photosensor Homolog from Burkholderia multivorans

Journal of Bacteriology ◽

10.1128/jb.00285-18 ◽

2018 ◽

Vol 200 (24) ◽

Cited By ~ 3

Author(s):

Satoru Sumi ◽

Hatsumi Shiratori-Takano ◽

Kenji Ueda ◽

Hideaki Takano

Keyword(s):

Constitutive Expression ◽

Light Response ◽

Binding Activity ◽

Binding Domain ◽

Class Iii ◽

Promoter Regions ◽

Content Type ◽

Burkholderia Multivorans ◽

Dna Binding Activity ◽

And Function

ABSTRACT The LitR/CarH protein family is an adenosyl B12 (AdoB12)-dependent photoreceptor family with DNA-binding activity, and its homologs are widely distributed in the genomes of diverse bacterial genera. In this investigation, we studied the role and functions of a LitR homolog from a Gram-negative soil bacterium, Burkholderia multivorans, which does not possess an AdoB12-binding domain. Transcriptome analysis indicated the existence of 19 light-induced genes, including folE2, cfaB, litS, photolyase gene phrB2, and cryB, located in the region flanking litR. Disruption of litR caused constitutive expression of all the light-inducible genes, while mutation in the light-induced sigma factor gene, litS, abolished the transcription of the phrB2 operon and the cfa operon, indicating that LitR and LitS play a central role in light-inducible transcription. A gel shift assay showed that recombinant protein LitR specifically binds to the promoter regions of litR and the folE2 operon, and its binding was weakened by UV-A illumination. LitR absorbs light at maximally near 340 nm and exhibited a photocyclic response and light-dependent dissociation of multimer into tetramer. The litR mutant produced a 20-fold-higher intracellular level of folate than that of the wild-type strain. Thus, the evidence suggests that LitR light-dependently regulates the transcription of litR itself and the folE2 operon, resulting in the production of folate, and then the expressed RNA polymerase complex containing σLitS directs the transcription of the phrB2 operon and the cfa operon. These light-dependent characteristics suggest that class III LitR, in complex with a UV-A-absorbing molecule, follows a novel light-sensing mechanism. IMPORTANCE Members of the LitR/CarH family are adenosyl B12-based photosensory transcriptional regulator involved in light-inducible carotenoid production in nonphototrophic bacteria. Our study provides the first evidence of the involvement of a class III LitR, which lacks an adenosyl B12-binding domain in the light response of Burkholderia multivorans belonging to betaproteobacteria. Our biochemical analysis suggests that class III LitR protein exhibits features as a photosensor including absorption of light at the UV-A region (λmax = ca. 340 nm), photocyclic response, and light-dependent dissociation. This suggests that class III LitR associates with a UV-A-absorbing molecule, and it has a photosensing mechanism distinguishable from that of the B12-based type.

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