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Journal articles on the topic 'HTH Domain'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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1

Abu-Shaar, M., and R. S. Mann. "Generation of multiple antagonistic domains along the proximodistal axis during Drosophila leg development." Development 125, no. 19 (1998): 3821–30. http://dx.doi.org/10.1242/dev.125.19.3821.

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homothorax (hth) is a Drosophila member of the Meis family of homeobox genes. hth function is required for the nuclear localization of the Hox cofactor Extradenticle (EXD). We show here that there is also a post-transcriptional control of HTH by exd: exd activity is required for the apparent stability of the HTH protein. In leg imaginal discs, hth expression is limited to the domain of exd function and this domain is complementary to the domain in which the Wingless (WG) and Decapentaplegic (DPP) signals are active. We demonstrate that WG and DPP act together through their targets Distal-less

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2

Kurant, Estee, Dan Eytan, and Adi Salzberg. "Mutational Analysis of the Drosophila homothorax Gene." Genetics 157, no. 2 (2001): 689–98. http://dx.doi.org/10.1093/genetics/157.2.689.

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Abstract The homothorax (hth) gene is involved in multiple aspects of embryonic and adult fly development. It encodes a homeodomain-containing protein of the MEIS family and was shown to regulate the subcellular localization of the homeotic protein cofactor Extradenticle (EXD). The HTH protein contains a TALE class homeodomain and a conserved MH domain, which is required for its interaction with EXD. In this work, we describe the structure of the hth locus, characterize at the molecular level a collection of mutant alleles of hth, and discuss the correlation between the identified structural d

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3

Roma, Josep, Ester Saus, Marc Cuadros, Jaume Reventós, Josep Sánchez de Toledo, and Soledad Gallego. "Characterisation of novel splicing variants of the tyrosine hydroxylase C-terminal domain in human neuroblastic tumours." Biological Chemistry 388, no. 4 (2007): 419–26. http://dx.doi.org/10.1515/bc.2007.041.

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Abstract Alternative splicing of human tyrosine hydroxylase (hTH) transcripts appears to occur mainly in the N-terminal domain, giving rise to at least eight different isoforms. We recently reported the existence of hTH transcript variants resulting from splicing of exons 8 and 9, within a region previously thought to be constant. The mRNA distribution of these novel hTH isoforms in neuroblastic tumours and in foetal adrenal glands was analysed by conventional and real-time RT-PCR. The presence of the target protein was determined by Western blotting, immunoprecipitation and protein analysis.

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Prolič-Kalinšek, Maruša, Alexander N. Volkov, San Hadži, et al. "Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7." Acta Crystallographica Section D Structural Biology 79, no. 3 (2023): 245–58. http://dx.doi.org/10.1107/s2059798323001249.

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YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA-binding protein and recognizes a 5′-TTGATTN6AATCAA-3′ inverted repeat. The DNA-binding domain is a helix–turn–helix (HTH)-containing POU domain and is followed by a long α-helix (α6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α2 and the recognition helix α3 in the HTH motif is unusually long compared with typical HTH motifs, and is highly variable in s

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5

Inbal, Adi, Naomi Halachmi, Charna Dibner, Dale Frank, and Adi Salzberg. "Genetic evidence for the transcriptional-activating function of Homothorax during adult fly development." Development 128, no. 18 (2001): 3405–13. http://dx.doi.org/10.1242/dev.128.18.3405.

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Homothorax (HTH) is a homeobox-containing protein, which plays multiple roles in the development of the embryo and the adult fly. HTH binds to the homeotic cofactor Extradenticle (EXD) and translocates it to the nucleus. Its function within the nucleus is less clear. It was shown, mainly by in vitro studies, that HTH can bind DNA as a part of ternary HTH/EXD/HOX complexes, but little is known about the transcription regulating function of HTH-containing complexes in the context of the developing fly. Here we present genetic evidence, from in vivo studies, for the transcriptional-activating fun

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6

Jun, S., and C. Desplan. "Cooperative interactions between paired domain and homeodomain." Development 122, no. 9 (1996): 2639–50. http://dx.doi.org/10.1242/dev.122.9.2639.

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The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs, the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical s

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7

Ryoo, H. D., T. Marty, F. Casares, M. Affolter, and R. S. Mann. "Regulation of Hox target genes by a DNA bound Homothorax/Hox/Extradenticle complex." Development 126, no. 22 (1999): 5137–48. http://dx.doi.org/10.1242/dev.126.22.5137.

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To regulate their target genes, the Hox proteins of Drosophila often bind to DNA as heterodimers with the homeodomain protein Extradenticle (EXD). For EXD to bind DNA, it must be in the nucleus, and its nuclear localization requires a third homeodomain protein, Homothorax (HTH). Here we show that a conserved N-terminal domain of HTH directly binds to EXD in vitro, and is sufficient to induce the nuclear localization of EXD in vivo. However, mutating a key DNA binding residue in the HTH homeodomain abolishes many of its in vivo functions. HTH binds to DNA as part of a HTH/Hox/EXD trimeric compl

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8

Li, Jincheng, Xudong Wang, Weimin Gong, Chunyan Niu, and Min Zhang. "Crystallization and preliminary X-ray analysis of Rv1674c fromMycobacterium tuberculosis." Acta Crystallographica Section F Structural Biology Communications 71, no. 3 (2015): 354–57. http://dx.doi.org/10.1107/s2053230x15001028.

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Adaptations to hypoxia play an important role inMycobacterium tuberculosispathogenesis. Rv0324, which contains an HTH DNA-binding domain and a rhodanese domain, is one of the key transcription regulators in response to hypoxia.M. tuberculosisRv1674c is a homologue of Rv0324. To understand the interdomain interaction and regulation of the HTH domain and the rhodanese domain, recombinant Rv1674c protein was purified and crystallized by the vapour-diffusion method. The crystals diffracted to 2.25 Å resolution. Preliminary diffraction analysis suggests that the crystals belonged to space groupP312

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9

Anantharaman, Vivek, Dapeng Zhang, and L. Aravind. "OST-HTH: a novel predicted RNA-binding domain." Biology Direct 5, no. 1 (2010): 13. http://dx.doi.org/10.1186/1745-6150-5-13.

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10

Crater, Dinene L., and Charles P. Moran. "Identification of a DNA Binding Region in GerE fromBacillus subtilis." Journal of Bacteriology 183, no. 14 (2001): 4183–89. http://dx.doi.org/10.1128/jb.183.14.4183-4189.2001.

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ABSTRACT Proteins that have a structure similar to those of LuxR and FixJ comprise a large subfamily of transcriptional activator proteins. Most members of the LuxR-FixJ family contain a similar amino-terminal receiver domain linked by a small region to a carboxy-terminal domain that contains an amino acid sequence similar to the helix-turn-helix (HTH) motif found in other DNA-binding proteins. GerE fromBacillus subtilis is the smallest member of the LuxR-FixJ family. Its 74-amino-acid sequence is similar over its entire length to the DNA binding region of this protein family, including the HT

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11

Calvo, Ana C., Angel L. Pey, Antonio Miranda-Vizuete, Anne P. Døskeland, and Aurora Martinez. "Divergence in enzyme regulation between Caenorhabditis elegans and human tyrosine hydroxylase, the key enzyme in the synthesis of dopamine." Biochemical Journal 434, no. 1 (2011): 133–41. http://dx.doi.org/10.1042/bj20101561.

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TH (tyrosine hydroxylase) is the rate-limiting enzyme in the synthesis of catecholamines. The cat-2 gene of the nematode Caenorhabditis elegans is expressed in mechanosensory dopaminergic neurons and has been proposed to encode a putative TH. In the present paper, we report the cloning of C. elegans full-length cat-2 cDNA and a detailed biochemical characterization of the encoded CAT-2 protein. Similar to other THs, C. elegans CAT-2 is composed of an N-terminal regulatory domain followed by a catalytic domain and a C-terminal oligomerization domain and shows high substrate specificity for L-ty

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12

Vahling, Cheryl M., and Kevin S. McIver. "Domains Required for Transcriptional Activation Show Conservation in the Mga Family of Virulence Gene Regulators." Journal of Bacteriology 188, no. 3 (2006): 863–73. http://dx.doi.org/10.1128/jb.188.3.863-873.2006.

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ABSTRACT Mga, or the multigene regulator of the group A streptococcus (GAS) (Streptococcus pyogenes), is a transcriptional regulator of virulence genes important for colonization and immune evasion. All serotypes of the GAS possess one of two divergent mga alleles (mga-1 or mga-2), and orthologues of Mga have also been identified in other pathogenic streptococci. To date, the only functional motifs established within Mga are two amino-terminal DNA-binding domains (HTH-3 and HTH-4). To uncover novel domains, a random mutagenesis screen using an M6 Mga (mga-1) was undertaken to find mutations le

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Kataoka, Masakazu, Takeshi Tanaka, Toshiyuki Kohno, and Yusuke Kajiyama. "The Carboxyl-Terminal Domain of TraR, a Streptomyces HutC Family Repressor, Functions in Oligomerization." Journal of Bacteriology 190, no. 21 (2008): 7164–69. http://dx.doi.org/10.1128/jb.00843-08.

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ABSTRACT Efficient conjugative transfer of the Streptomyces plasmid pSN22 is accomplished by regulated expression of the tra operon genes, traA, traB, and spdB. The TraR protein is the central transcriptional repressor regulating the expression of the tra operon and itself and is classified as a member of the HutC subfamily in the helix-turn-helix (HTH) GntR protein family. Sequence information predicts that the N-terminal domain (NTD) of TraR, containing an HTH motif, functions in binding of DNA to the cis element; however, the function of the C-terminal region remains obscure, like that for

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14

Charity, Julia A., Peter Hughes, Marilyn A. Anderson, Dennis J. Bittisnich, Malcolm Whitecross та T. J. V. Higgins. "Pest and disease protection conferred by expression of barley β - hordothionin and Nicotiana alata proteinase inhibitor genes in transgenic tobacco". Functional Plant Biology 32, № 1 (2005): 35. http://dx.doi.org/10.1071/fp04105.

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Proteinase inhibitors and thionins are among the many proteins thought to have a role in plant defence against pests and pathogens. Complementary DNA clones encoding the precursors of a multi-domain proteinase inhibitor from Nicotiana alata Link et Otto (NA-PI) (Mr approximately 43 000) and a β-hordothionin (β-HTH) (Mr approximately 13 000) from barley, were linked to constitutive promoters and subsequently transferred by Agrobacterium-mediated transformation into tobacco. The NA-PI and β-HTH precursor proteins were synthesised and post-translationally processed in transgenic tobacco and accum

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15

Jiménez, Rafael, Sara B. Cruz-Migoni, Alejandro Huerta-Saquero, Víctor H. Bustamante, and José L. Puente. "Molecular Characterization of GrlA, a Specific Positive Regulator of ler Expression in Enteropathogenic Escherichia coli." Journal of Bacteriology 192, no. 18 (2010): 4627–42. http://dx.doi.org/10.1128/jb.00307-10.

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ABSTRACT Enteropathogenic Escherichia coli (EPEC) infections are characterized by the formation of attaching and effacing (A/E) lesions on the surfaces of infected epithelial cells. The genes required for the formation of A/E lesions are located within the locus of enterocyte effacement (LEE). Ler is the key regulatory factor controlling the expression of LEE genes. Expression of the ler gene is positively regulated by GrlA, which is encoded by the LEE. Here, we analyze the mechanism by which GrlA positively regulates ler expression and show that in the absence of H-NS, GrlA is no longer essen

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16

Shen, Yingzi, Jiaping Wei, Shuang Wang, et al. "The Copper Chaperone Protein Gene GmATX1 Promotes Seed Vigor and Seedling Tolerance under Heavy Metal and High Temperature and Humidity Stresses in Transgenic Arabidopsis." Plants 11, no. 10 (2022): 1325. http://dx.doi.org/10.3390/plants11101325.

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Abiotic stresses such as high temperature, high humidity, and heavy metals are important factors that affect seed development and quality, and restrict yield in soybean. The ATX1-type copper chaperones are an important type of proteins that are used for maintaining intracellular copper ion homeostasis. In our previous study, a copper chaperone protein GmATX1 was identified in developing seeds of soybean under high temperature and humidity (HTH) stresses. In this study, the GmATX1 gene was isolated, and multiple alignment analysis showed that its encoding protein shared high sequence identities

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Liu, Sushuang, Yanmin Liu, Chundong Liu, Yang Li, Feixue Zhang, and Hao Ma. "Isolation and Characterization of the GmMT-II Gene and Its Role in Response to High Temperature and Humidity Stress in Glycine max." Plants 11, no. 11 (2022): 1503. http://dx.doi.org/10.3390/plants11111503.

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Metallothioneins (MTs) are polypeptide-encoded genes involved in plant growth, development, seed formation, and diverse stress response. High temperature and humidity stress (HTH) reduce seed development and maturity of the field-grown soybean, which also leads to seed pre-harvest deterioration. However, the function of MTs in higher plants is still largely unknown. Herein, we isolated and characterized the soybean metallothionein II gene. The full-length fragment is 255 bp and encodes 85 amino acids and contains the HD domain and the N-terminal non-conservative region. The subcellular locatio

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Kubíková, Jana, Rebecca Reinig, Harpreet Kaur Salgania, and Mandy Jeske. "LOTUS-domain proteins - developmental effectors from a molecular perspective." Biological Chemistry 402, no. 1 (2020): 7–23. http://dx.doi.org/10.1515/hsz-2020-0270.

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AbstractThe LOTUS domain (also known as OST-HTH) is a highly conserved protein domain found in a variety of bacteria and eukaryotes. In animals, the LOTUS domain is present in the proteins Oskar, TDRD5/Tejas, TDRD7/TRAP/Tapas, and MARF1/Limkain B1, all of which play essential roles in animal development, in particular during oogenesis and/or spermatogenesis. This review summarizes the diverse biological as well as molecular functions of LOTUS-domain proteins and discusses their roles as helicase effectors, post-transcriptional regulators, and critical cofactors of piRNA-mediated transcript sil

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Park, Jin-Young, Hyo Jung Kim, Chinar Pathak, et al. "Induced DNA bending by unique dimerization of HigA antitoxin." IUCrJ 7, no. 4 (2020): 748–60. http://dx.doi.org/10.1107/s2052252520006466.

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The bacterial toxin–antitoxin (TA) system regulates cell growth under various environmental stresses. Mycobacterium tuberculosis, the causative pathogen of tuberculosis (TB), has three HigBA type II TA systems with reverse gene organization, consisting of the toxin protein HigB and labile antitoxin protein HigA. Most type II TA modules are transcriptionally autoregulated by the antitoxin itself. In this report, we first present the crystal structure of the M. tuberculosis HigA3 antitoxin (MtHigA3) and MtHigA3 bound to its operator DNA complex. We also investigated the interaction between MtHig

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20

LI, Shi-Sheng, Joachim GULLBO, Petra LINDHOLM, et al. "Ligatoxin B, a new cytotoxic protein with a novel helix–turn–helix DNA-binding domain from the mistletoe Phoradendron liga." Biochemical Journal 366, no. 2 (2002): 405–13. http://dx.doi.org/10.1042/bj20020221.

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A new basic protein, designated ligatoxin B, containing 46 amino acid residues has been isolated from the mistletoe Phoradendron liga (Gill.) Eichl. (Viscaceae). The protein's primary structure, determined unambiguously using a combination of automated Edman degradation, trypsin enzymic digestion, and tandem MS analysis, was 1–KSCCPSTTAR–NIYNTCRLTG–ASRSVCASLS–GCKIISGSTC–DSGWNH–46. Ligatoxin B exhibited in vitro cytotoxic activities on the human lymphoma cell line U-937-GTB and the primary multidrug-resistant renal adenocarcinoma cell line ACHN, with IC50 values of 1.8μM and 3.2μM respectively.

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He, Qing, Kang Wang, Tiantian Su, Feng Wang, Lichuan Gu, and Sujuan Xu. "Crystal structure of the N-terminal domain of VqsR fromPseudomonas aeruginosaat 2.1 Å resolution." Acta Crystallographica Section F Structural Biology Communications 73, no. 7 (2017): 431–36. http://dx.doi.org/10.1107/s2053230x17009025.

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VqsR is a quorum-sensing (QS) transcriptional regulator which controls QS systems (las,rhlandpqs) by directly downregulating the expression ofqscRinPseudomonas aeruginosa. As a member of the LuxR family of proteins, VqsR shares the common motif of a helix–turn–helix (HTH)-type DNA-binding domain at the C-terminus, while the function of its N-terminal domain remains obscure. Here, the crystal structure of the N-terminal domain of VqsR (VqsR-N; residues 1–193) was determined at a resolution of 2.1 Å. The structure is folded into a regular α–β–α sandwich topology, which is similar to the ligand-b

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Veraksa, A., N. McGinnis, X. Li, J. Mohler, and W. McGinnis. "Cap ‘n’ collar B cooperates with a small Maf subunit to specify pharyngeal development and suppress deformed homeotic function in the Drosophila head." Development 127, no. 18 (2000): 4023–37. http://dx.doi.org/10.1242/dev.127.18.4023.

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The basic-leucine zipper protein Cap ‘n’ collar B (CncB) suppresses the segmental identity function of the Hox gene Deformed (Dfd) in the mandibular segment of Drosophila embryos. CncB is also required for proper development of intercalary, labral and mandibular structures. In this study, we provide evidence that the CncB-mediated suppression of Dfd requires the Drosophila homolog of the mammalian small Maf proteins, Maf-S, and that the suppression occurs even in the presence of high amounts of Dfd protein. Interestingly, the CncB/Maf-S suppressive effect can be partially reversed by overexpre

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Akiyama, Tomonori, Yusuke Yamada, Naoki Takaya, Shinsaku Ito, Yasuyuki Sasaki, and Shunsuke Yajima. "Crystal structure of an IclR homologue fromMicrobacteriumsp. strain HM58-2." Acta Crystallographica Section F Structural Biology Communications 73, no. 1 (2017): 16–23. http://dx.doi.org/10.1107/s2053230x16019208.

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The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix–turn–helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) fromMicrobacteriumsp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments

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Moinier, Danielle, Deborah Byrne, Agnès Amouric, and Violaine Bonnefoy. "How the RegBA Redox Responding System Controls Iron and Sulfur Oxidation in Acidithiobacillus ferrooxidans." Advanced Materials Research 825 (October 2013): 186–89. http://dx.doi.org/10.4028/www.scientific.net/amr.825.186.

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Valuable metals as well as ferrous iron and sulfur compounds are released from ore by ferric iron and sulfuric acid chemical attack. Biomining microorganisms allow the recycling of these products by oxidizing ferrous iron and/or sulfur compounds. The energy released from the oxidation of these substrates is used for the growth of the acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans. The respiratory pathways involved in these respiratory processes have been deciphered and the expression of the genes encoding these redox proteins is dependent on the electron donor prese

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McGee, Clayton J., and Susan C. van den Heever. "Latent Heating and Mixing due to Entrainment in Tropical Deep Convection." Journal of the Atmospheric Sciences 71, no. 2 (2014): 816–32. http://dx.doi.org/10.1175/jas-d-13-0140.1.

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Abstract Recent studies have noted the role of latent heating above the freezing level in reconciling Riehl and Malkus' hot tower hypothesis (HTH) with evidence of diluted tropical deep convective cores. This study evaluates recent modifications to the HTH through Lagrangian trajectory analysis of deep convective cores in an idealized, high-resolution cloud-resolving model (CRM) simulation that uses a sophisticated two-moment microphysical scheme. A line of tropical convective cells develops within a finer nested grid whose boundary conditions are obtained from a large-domain CRM simulation ap

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Martínez-Santos, Verónica I., Abraham Medrano-López, Zeus Saldaña, Jorge A. Girón, and José L. Puente. "Transcriptional Regulation of theecpOperon by EcpR, IHF, and H-NS in Attaching and Effacing Escherichia coli." Journal of Bacteriology 194, no. 18 (2012): 5020–33. http://dx.doi.org/10.1128/jb.00915-12.

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ABSTRACTEnteropathogenic (EPEC) and enterohemorrhagic (EHEC)Escherichia coliare clinically important diarrheagenic pathogens that adhere to the intestinal epithelial surface. TheE. colicommon pili (ECP), or meningitis-associated and temperature-regulated (MAT) fimbriae, are ubiquitous among both commensal and pathogenicE. colistrains and play a role as colonization factors by promoting the interaction between bacteria and host epithelial cells and favoring interbacterial interactions in biofilm communities. The first gene of theecpoperon encodes EcpR (also known as MatA), a proposed regulatory

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Rieger, Janine, Michael Fitz, Stefan Markus Fischer, et al. "Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods." Genes 14, no. 8 (2023): 1638. http://dx.doi.org/10.3390/genes14081638.

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Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure

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Song, Shihao, Xiuyun Sun, Quan Guo, et al. "An anthranilic acid-responsive transcriptional regulator controls the physiology and pathogenicity of Ralstonia solanacearum." PLOS Pathogens 18, no. 5 (2022): e1010562. http://dx.doi.org/10.1371/journal.ppat.1010562.

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Quorum sensing (QS) is widely employed by bacterial cells to control gene expression in a cell density-dependent manner. A previous study revealed that anthranilic acid from Ralstonia solanacearum plays a vital role in regulating the physiology and pathogenicity of R. solanacearum. We reported here that anthranilic acid controls the important biological functions and virulence of R. solanacearum through the receptor protein RaaR, which contains helix-turn-helix (HTH) and LysR substrate binding (LysR_substrate) domains. RaaR regulates the same processes as anthranilic acid, and both are present

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Šoltysová, Markéta, Irena Sieglová, Milan Fábry, Jiří Brynda, Jana Škerlová, and Pavlína Řezáčová. "Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family." Acta Crystallographica Section D Structural Biology 77, no. 11 (2021): 1411–24. http://dx.doi.org/10.1107/s2059798321009633.

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The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N-terminal DNA-binding domains of bsDeoR and

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Lu, Huizhi, Liangyan Wang, Shengjie Li, et al. "Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO." Nucleic Acids Research 47, no. 18 (2019): 9925–33. http://dx.doi.org/10.1093/nar/gkz720.

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Abstract DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-termina

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Orłowski, Marek, Katarzyna Popławska, Joanna Pieprzyk, et al. "Molecular determinants of Drosophila immunophilin FKBP39 nuclear localization." Biological Chemistry 399, no. 5 (2018): 467–84. http://dx.doi.org/10.1515/hsz-2017-0251.

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AbstractFK506-binding proteins (FKBPs) belong to a distinct class of immunophilins that interact with immunosuppressants. They use their peptidyl-prolyl isomerase (PPIase) activity to catalyze thecis-transconversion of prolyl bonds in proteins during protein-folding events. FKBPs also act as a unique group of chaperones. TheDrosophila melanogasterpeptidyl-prolylcis-transisomerase FK506-binding protein of 39 kDa (FKBP39) is thought to act as a transcriptional modulator of gene expression in 20-hydroxyecdysone and juvenile hormone signal transduction. The aim of this study was to analyze the mol

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Yin, Yanping, Youyun Yang, Xuwu Xiang, et al. "Insight into the Dual Functions of Bacterial Enhancer-Binding Protein Rrp2 of Borrelia burgdorferi." Journal of Bacteriology 198, no. 10 (2016): 1543–52. http://dx.doi.org/10.1128/jb.01010-15.

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ABSTRACTIt is well established that the RpoN-RpoS sigma factor (σ54-σS) cascade plays an essential role in differential gene expression during the enzootic cycle ofBorrelia burgdorferi, the causative agent of Lyme disease. The RpoN-RpoS pathway is activated by the response regulator/σ54-dependent activator (also called bacterial enhancer-binding protein [bEBP]) Rrp2. One unique feature of Rrp2 is that this activator is essential for cell replication, whereas RpoN-RpoS is dispensable for bacterial growth. How Rrp2 controls cell replication, a function that is independent of RpoN-RpoS, remains t

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Knutson, Bruce A., Rachel McNamar, and Lawrence I. Rothblum. "Dynamics of the RNA polymerase I TFIIF/TFIIE-like subcomplex: a mini-review." Biochemical Society Transactions 48, no. 5 (2020): 1917–27. http://dx.doi.org/10.1042/bst20190848.

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RNA polymerase I (Pol I) is the most specialized eukaryotic Pol. It is only responsible for the synthesis of pre-ribosomal RNA (rRNA), the precursor of 18S, 5.8S and 28S rRNA, the most abundant cellular RNA types. Aberrant Pol I transcription is observed in a wide variety of cancers and its down-regulation is associated with several genetic disorders. The regulation and mechanism of Pol I transcription is increasing in clarity given the numerous high-resolution Pol I structures that have helped bridge seminal genetic and biochemical findings in the field. Here, we review the multifunctional ro

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Bartosik, A. A., J. Mierzejewska, C. M. Thomas, and G. Jagura-Burdzy. "ParB deficiency in Pseudomonas aeruginosa destabilizes the partner protein ParA and affects a variety of physiological parameters." Microbiology 155, no. 4 (2009): 1080–92. http://dx.doi.org/10.1099/mic.0.024661-0.

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Deletions leading to complete or partial removal of ParB were introduced into the Pseudomonas aeruginosa chromosome. Fluorescence microscopy of fixed cells showed that ParB mutants lacking the C-terminal domain or HTH motif formed multiple, less intense foci scattered irregularly, in contrast to the one to four ParB foci per cell symmetrically distributed in wild-type P. aeruginosa. All parB mutations affected both bacterial growth and swarming and swimming motilities, and increased the production of anucleate cells. Similar effects were observed after inactivation of parA of P. aeruginosa. As

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ZeinEldin, Ramadan A., Marwa M. Ahmed, Wael S. Hassanein, et al. "Diversity and Distribution Characteristics of Viruses from Soda Lakes." Genes 14, no. 2 (2023): 323. http://dx.doi.org/10.3390/genes14020323.

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Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single

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Chagraoui, Jalila, Sherry Niessen, Julie Lessard, et al. "p120E4F-1: A Novel Candidate Factor for Mediating Bmi-1 Function in Hematopoietic Stem Cells." Blood 104, no. 11 (2004): 370. http://dx.doi.org/10.1182/blood.v104.11.370.370.

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Abstract We have recently demonstrated that the Polycomb group (Pc-G) gene bmi-1 is essential for the self-renewal/proliferation of both normal and leukemic hematopoietic stem cells (HSCs). Interestingly, none of the gene products with which Bmi-1 interacts are expressed in this cellular compartment. Therefore, it has been postulated that the proliferative function of Bmi-1 in HSCs is mediated through its interaction with non-identified partners. A yeast two-hybrid assay, using Bmi-1 as bait to screen a fetal liver cDNA library, led to the isolation of p120E4F-1, previously identified as a neg

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Boudsocq, François, Maya Salhi, Sophie Barbe, and Jean-Yves Bouet. "Three ParA Dimers Cooperatively Assemble on Type Ia Partition Promoters." Genes 12, no. 9 (2021): 1345. http://dx.doi.org/10.3390/genes12091345.

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Accurate DNA segregation is essential for faithful inheritance of genetic material. In bacteria, this process is mainly ensured by partition systems composed of two proteins, ParA and ParB, and a centromere site. Auto-regulation of Par operon expression is important for efficient partitioning and is primarily mediated by ParA for type Ia plasmid partition systems. For the F-plasmid, four ParAF monomers were proposed to bind to four repeated sequences in the promoter region. By contrast, using quantitative surface-plasmon-resonance, we showed that three ParAF dimers bind to this region. We unco

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Ye, Fuzhou, Chao Wang, Veerendra Kumar, Lianhui Zhang, and Yonggui Gao. "BswR controls bacterial motility and biofilm formation via modulation RNA rsmZ." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C216. http://dx.doi.org/10.1107/s2053273314097836.

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Pseudomonas aeruginosa relies on cell motility and ability to form biofilms to establish infections, however, the mechanism of regulation remains obscure. Here we report that BswR, a XRE (Xenobiotic Response Element) type transcriptional regulator, plays a critical role in regulation of bacterial motility and biofilm formation in P. aeruginosa. Transcriptomic and biochemical analyses showed that BswR counteracts the repressor activity of MvaT, controls the transcription of small RNA rsmZ and regulates the biogenesis of bacterial flagella. The crystal structure of BswR was determined at 2.3 Å r

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Parker, Ernest T., Christopher B. Doering, and Pete Lollar. "Factor VIIIa Decay Due to A2 Subunit Dissociation Is Regulated by the A1 Domain." Blood 106, no. 11 (2005): 1009. http://dx.doi.org/10.1182/blood.v106.11.1009.1009.

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Abstract FVIII contains three homologous A domains, two homologous C domains and a single B domain. The B domain and an activation peptide between the B and A3 domains are released during the activation of fVIII by thrombin. The resulting fVIIIa molecule has a heterotrimeric A1/A2/A3-C1–C2 subunit structure. FVIIIa is unstable at physiological concentrations and pH due to dissociation of the A2 subunit from the A1/A3-C1–C2 dimer, which is three-fold faster in human fVIIIa than porcine fVIIIa. Fine regulation of fVIII activity appears to be important because plasma fVIII levels are positively c

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Zhang, Chen, Zhengfu Zhou, Wei Zhang, et al. "The Site-Directed A184S Mutation in the HTH Domain of the Global Regulator IrrE Enhances Deinococcus radiodurans R1 Tolerance to UV Radiation and MMC Shock." Journal of Microbiology and Biotechnology 25, no. 12 (2015): 2125–34. http://dx.doi.org/10.4014/jmb.1507.07008.

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Crater, Dinene L., and Charles P. Moran. "Two Regions of GerE Required for Promoter Activation in Bacillus subtilis." Journal of Bacteriology 184, no. 1 (2002): 241–49. http://dx.doi.org/10.1128/jb.184.1.241-249.2002.

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ABSTRACT GerE from Bacillus subtilis is the smallest member of the LuxR-FixJ family of transcription activators. Its 74-amino-acid sequence is similar over its entire length to the DNA binding domain of this protein family, including a putative helix-turn-helix (HTH) motif. In this report, we sought to define regions of GerE involved in promoter activation. We examined the effects of single alanine substitutions at 19 positions that were predicted by the crystal structure of GerE to be located on its surface. A single substitution of alanine for the phenylalanine at position 6 of GerE (F6A) re

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Xu, Xingya, and Mitsuhiro Yanagida. "Suppressor screening reveals common kleisin–hinge interaction in condensin and cohesin, but different modes of regulation." Proceedings of the National Academy of Sciences 116, no. 22 (2019): 10889–98. http://dx.doi.org/10.1073/pnas.1902699116.

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Cohesin and condensin play fundamental roles in sister chromatid cohesion and chromosome segregation, respectively. Both consist of heterodimeric structural maintenance of chromosomes (SMC) subunits, which possess a head (containing ATPase) and a hinge, intervened by long coiled coils. Non-SMC subunits (Cnd1, Cnd2, and Cnd3 for condensin; Rad21, Psc3, and Mis4 for cohesin) bind to the SMC heads. Here, we report a large number of spontaneous extragenic suppressors for fission yeast condensin and cohesin mutants, and their sites were determined by whole-genome sequencing. Mutants of condensin’s

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Wu, J., and S. M. Cohen. "Proximodistal axis formation in the Drosophila leg: subdivision into proximal and distal domains by Homothorax and Distal-less." Development 126, no. 1 (1999): 109–17. http://dx.doi.org/10.1242/dev.126.1.109.

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The developing legs of Drosophila are subdivided into proximal and distal domains by the activity of the homeodomain proteins Homothorax (Hth) and Distal-less (Dll). The expression domains of Dll and Hth are initially reciprocal. Wingless and Dpp define both domains by activating Dll and by repressing Hth in the distal region of the disc. Wg and Dpp do not act through Dll to repress Hth. Hth functions to reduce the sensitivity of proximal cells to Wg and Dpp. This serves to limit the effective range of these signals in regulating later-acting genes such as Dac. We present evidence that proxima

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Du, Wenhao, Haixia Zhu, Jiaqiang Qian, Dongmei Xue, Sen Zheng, and Qiang Huang. "Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State." International Journal of Molecular Sciences 24, no. 2 (2023): 1204. http://dx.doi.org/10.3390/ijms24021204.

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Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this stru

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Aravind, L., and Lakshminarayan M. Iyer. "The HARE-HTH and associated domains." Cell Cycle 11, no. 1 (2012): 119–31. http://dx.doi.org/10.4161/cc.11.1.18475.

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Jacob, Jansen, and Martin Drummond. "Construction of chimeric proteins from the ?;N-associated transcriptional activators VnfA and AnfA of Azotobacter vinelndii shows that the determinants of promoter specificity lie outside the'recognition'helix of the HTH motif in the C-terminal domain." Molecular Microbiology 10, no. 4 (1993): 813–21. http://dx.doi.org/10.1111/j.1365-2958.1993.tb00951.x.

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Schwarz, J. J., T. Chakraborty, J. Martin, J. M. Zhou, and E. N. Olson. "The basic region of myogenin cooperates with two transcription activation domains to induce muscle-specific transcription." Molecular and Cellular Biology 12, no. 1 (1992): 266–75. http://dx.doi.org/10.1128/mcb.12.1.266-275.1992.

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Myogenin is a skeletal muscle-specific transcription factor that can activate myogenesis when introduced into a variety of nonmuscle cell types. Activation of the myogenic program by myogenin is dependent on its binding to a DNA sequence known as an E box, which is associated with numerous muscle-specific genes. Myogenin shares homology with MyoD and other myogenic regulatory factors within a basic region and a helix-loop-helix (HLH) motif that mediate DNA binding and dimerization, respectively. Here we show that the basic region-HLH motif of myogenin alone lacks transcriptional activity and i

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Schwarz, J. J., T. Chakraborty, J. Martin, J. M. Zhou, and E. N. Olson. "The basic region of myogenin cooperates with two transcription activation domains to induce muscle-specific transcription." Molecular and Cellular Biology 12, no. 1 (1992): 266–75. http://dx.doi.org/10.1128/mcb.12.1.266.

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Myogenin is a skeletal muscle-specific transcription factor that can activate myogenesis when introduced into a variety of nonmuscle cell types. Activation of the myogenic program by myogenin is dependent on its binding to a DNA sequence known as an E box, which is associated with numerous muscle-specific genes. Myogenin shares homology with MyoD and other myogenic regulatory factors within a basic region and a helix-loop-helix (HLH) motif that mediate DNA binding and dimerization, respectively. Here we show that the basic region-HLH motif of myogenin alone lacks transcriptional activity and i

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Trujillo, Miguel A., Michiko Sakagashira, and Norman L. Eberhardt. "The Human Growth Hormone Gene Contains a Silencer Embedded within an Alu Repeat in the 3′-Flanking Region." Molecular Endocrinology 20, no. 10 (2006): 2559–75. http://dx.doi.org/10.1210/me.2006-0147.

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Abstract Alu family sequences are middle repetitive short interspersed elements (SINEs) dispersed throughout vertebrate genomes that can modulate gene transcription. The human (h) GH locus contains 44 complete and four partial Alu elements. An Sx Alu repeat lies in close proximity to the hGH-1 and hGH-2 genes in the 3′-flanking region. Deletion of the Sx Alu repeat in reporter constructs containing hGH-1 3′-flanking sequences increased reporter activity in transfected pituitary GC cells, suggesting this region contained a repressor element. Analysis of multiple deletion fragments from the 3′-f

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Brachner, Andreas, and Roland Foisner. "Evolvement of LEM proteins as chromatin tethers at the nuclear periphery." Biochemical Society Transactions 39, no. 6 (2011): 1735–41. http://dx.doi.org/10.1042/bst20110724.

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The nuclear envelope in eukaryotic cells has important roles in chromatin organization. The inner nuclear membrane contains over 60 transmembrane proteins. LEM [LAP2 (lamina-associated polypeptide 2)/emerin/MAN1] domain-containing proteins of the inner nuclear membrane are involved in tethering chromatin to the nuclear envelope and affect gene expression. They contain a common structural, bihelical motif, the so-called LEM domain, which mediates binding to a conserved chromatin protein, BAF (barrier to autointegration factor). Interestingly, this domain is highly related to other bihelical mot

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