scholarly journals Characterization of Two Dinoflagellate Cold Shock Domain Proteins

mSphere ◽  
2016 ◽  
Vol 1 (1) ◽  
Author(s):  
Mathieu Beauchemin ◽  
Sougata Roy ◽  
Sarah Pelletier ◽  
Alexandra Averback ◽  
Frederic Lanthier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Mobility Shift ◽  
Two Dimensional Gel Electrophoresis ◽  
Content Type ◽  
Cold Shock Domain ◽  
Cold Shock Domain Proteins ◽  
Specific Sequences

ABSTRACT Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists. Roughly two-thirds of the proteins annotated as transcription factors in dinoflagellate transcriptomes are cold shock domain-containing proteins (CSPs), an uncommon condition in eukaryotic organisms. However, no functional analysis has ever been reported for a dinoflagellate CSP, and so it is not known if they do in fact act as transcription factors. We describe here some of the properties of two CSPs from the dinoflagellate Lingulodinium polyedrum, LpCSP1 and LpCSP2, which contain a glycine-rich C-terminal domain and an N-terminal cold shock domain phylogenetically related to those in bacteria. However, neither of the two LpCSPs act like the bacterial CSP, since they do not functionally complement the Escherichia coli quadruple cold shock domain protein mutant BX04, and cold shock does not induce LpCSP1 and LpCSP2 to detectable levels, based on two-dimensional gel electrophoresis. Both CSPs bind to RNA and single-stranded DNA in a nonspecific manner in electrophoretic mobility shift assays, and both proteins also bind double-stranded DNA nonspecifically, albeit more weakly. These CSPs are thus unlikely to act alone as sequence-specific transcription factors. IMPORTANCE Dinoflagellate transcriptomes contain cold shock domain proteins as the major component of the proteins annotated as transcription factors. We show here that the major family of cold shock domain proteins in the dinoflagellate Lingulodinium do not bind specific sequences, suggesting that transcriptional control is not a predominant mechanism for regulating gene expression in this group of protists.

scholarly journals Assessing nucleic acid binding activity of four dinoflagellate cold shock domain proteins from Symbiodinium kawagutii and Lingulodinium polyedra

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bahareh Zaheri ◽  
David Morse
Keyword(s):  
Transcription Factors ◽  
Nucleic Acid ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Binding Activity ◽  
Dependent Manner ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Double Stranded Dna ◽  
Cold Shock Domain

Abstract Background Dinoflagellates have a generally large number of genes but only a small percentage of these are annotated as transcription factors. Cold shock domain (CSD) containing proteins (CSPs) account for roughly 60% of these. CSDs are not prevalent in other eukaryotic lineages, perhaps suggesting a lineage-specific expansion of this type of transcription factors in dinoflagellates, but there is little experimental data to support a role for dinoflagellate CSPs as transcription factors. Here we evaluate the hypothesis that dinoflagellate CSPs can act as transcription factors by binding double-stranded DNA in a sequence dependent manner. Results We find that both electrophoretic mobility shift assay (EMSA) competition experiments and selection and amplification binding (SAAB) assays indicate binding is not sequence specific for four different CSPs from two dinoflagellate species. Competition experiments indicate all four CSPs bind to RNA better than double-stranded DNA. Conclusion Dinoflagellate CSPs do not share the nucleic acid binding properties expected for them to function as bone fide transcription factors. We conclude the transcription factor complement of dinoflagellates is even smaller than previously thought suggesting that dinoflagellates have a reduced dependance on transcriptional control compared to other eukaryotes.

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

BioEssays ◽  
2010 ◽  
Vol 32 (2) ◽  
pp. 109-118 ◽  
Author(s):  
Marija Mihailovich ◽  
Cristina Militti ◽  
Toni Gabaldón ◽  
Fátima Gebauer
Keyword(s):  
Gene Expression ◽  
Cold Shock ◽  
Cold Shock Domain ◽  
Cold Shock Domain Proteins

scholarly journals FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Gaili Fan ◽  
Huawei Zheng ◽  
Kai Zhang ◽  
Veena Devi Ganeshan ◽  
Stephen Obol Opiyo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Family ◽  
Fusarium Graminearum ◽  
Target Genes ◽  
Homeobox Gene ◽  
Global Gene Expression ◽  
Binding Motifs ◽  
Content Type ◽  
Aerial Growth

ABSTRACT The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes. IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum. In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.

scholarly journals The Mycobacterium tuberculosis sRNA F6 regulates expression of groEL/S

2020 ◽  
Author(s):  
Joanna Houghton ◽  
Angela Rodgers ◽  
Graham Rose ◽  
Kristine B. Arnvig
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Small Rnas ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Control Of Gene Expression ◽  
Rna Biology ◽  
Mouse Model Of Infection

ABSTRACTAlmost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA, F6, and show it to be dependent on SigF for expression and significantly induced during in vitro starvation and in a mouse model of infection. However, we found no evidence of attenuation of a ΔF6 strain within the first 20 weeks of infection. A further exploration of F6 using in vitro models of infection suggests a role for F6 as a highly specific regulator of the heat shock repressor, HrcA. Our results point towards a role for F6 during periods of low metabolic activity similar to cold shock and associated with nutrient starvation such as that found in human granulomas in later stages of infection.

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

Usage of cold shock domain proteins for improvement of frost hardiness in plant biotechnology

2013 ◽  
Vol 39 (4) ◽  
pp. 315-317
Author(s):  
V. V. Taranov ◽  
M. V. Berdnikova ◽  
N. E. Zlobin ◽  
A. V. Babakov
Keyword(s):  
Cold Shock ◽  
Plant Biotechnology ◽  
Frost Hardiness ◽  
Cold Shock Domain ◽  
Cold Shock Domain Proteins

scholarly journals Interaction between STAT-3 and HNF-3 Leads to the Activation of Liver-Specific Hepatitis B Virus Enhancer 1 Function

2002 ◽  
Vol 76 (6) ◽  
pp. 2721-2729 ◽  
Author(s):  
Gulam Waris ◽  
Aleem Siddiqui
Keyword(s):  
Gene Expression ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Transcriptional Control ◽  
Viral Gene Expression ◽  
Cooperative Interaction ◽  
Viral Gene ◽  
Mobility Shift ◽  
B Virus ◽  
Stimulation Of

ABSTRACT The signal transducer and activator of transcription 3 (STAT-3), a member of the STAT family of proteins, binds to a large number of transcriptional control elements and regulates gene expression in response to cytokines. While it binds to its cognate nucleotide sequences, it has been recently shown to directly interact with other transcriptional factors in the absence of DNA. We report here one such novel interaction between STAT-3 and hepatocyte nuclear factor 3 (HNF-3) in the absence of DNA. We have identified a STAT-3 binding site within the core domain of hepatitis B virus (HBV) enhancer 1. The HBV enhancer 1 DNA-STAT-3 protein interaction is shown to be stimulated by interleukin-6 (IL-6) and epidermal growth factor, which leads to an overall stimulation of HBV enhancer 1 function and viral gene expression. Using mobility shift assays and transient transfection schemes, we demonstrate a cooperative interaction between HNF-3 and STAT-3 in mediating the cytokine-mediated HBV enhancer function. Cytokine stimulation of HBV gene expression represents an important regulatory scheme of direct relevance to liver disease pathogenesis associated with HBV infection.

scholarly journals Hierarchical Transcriptional Control of the LuxR Quorum-Sensing Regulon of Vibrio harveyi

2020 ◽  
Vol 202 (14) ◽  
Author(s):  
Ryan R. Chaparian ◽  
Alyssa S. Ball ◽  
Julia C. van Kessel
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Quorum Sensing ◽  
Cell Density ◽  
Regulatory Networks ◽  
Vibrio Harveyi ◽  
Sugar Transport ◽  
Content Type ◽  
Second Tier

ABSTRACT In vibrios, quorum sensing controls hundreds of genes that are required for cell density-specific behaviors including bioluminescence, biofilm formation, competence, secretion, and swarming motility. The central transcription factor in the quorum-sensing pathway is LuxR/HapR, which directly regulates ∼100 genes in the >400-gene regulon of Vibrio harveyi. Among these directly controlled genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the LuxR regulon. We confirmed that LuxR binds to the promoters of these genes in vitro and quantified the extent of LuxR activation or repression of transcript levels. Transcriptome sequencing (RNA-seq) indicates that most of these transcriptional regulators control only a few genes, with the exception of MetJ, which is a global regulator. The genes regulated by these transcription factors are predicted to be involved in methionine and thiamine biosynthesis, membrane stability, RNA processing, c-di-GMP degradation, sugar transport, and other cellular processes. These data support a hierarchical model in which LuxR directly regulates 15 transcription factors that drive the second level of the gene expression cascade to influence cell density-dependent metabolic states and behaviors in V. harveyi. IMPORTANCE Quorum sensing is important for survival of bacteria in nature and influences the actions of bacterial groups. In the relatively few studied examples of quorum-sensing-controlled genes, these genes are associated with competition or cooperation in complex microbial communities and/or virulence in a host. However, quorum sensing in vibrios controls the expression of hundreds of genes, and their functions are mostly unknown or uncharacterized. In this study, we identify the regulators of the second tier of gene expression in the quorum-sensing system of the aquaculture pathogen Vibrio harveyi. Our identification of regulatory networks and metabolic pathways controlled by quorum sensing can be extended and compared to other Vibrio species to understand the physiology, ecology, and pathogenesis of these organisms.

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