scholarly journals Evolution of a New Testis-Specific Functional Promoter Within the Highly Conserved Map2k7 Gene of the Mouse

2022 ◽  
Vol 12 ◽  
Author(s):  
Tobias Heinen ◽  
Chen Xie ◽  
Maryam Keshavarz ◽  
Dominik Stappert ◽  
Sven Künzel ◽  
...  

Map2k7 (synonym Mkk7) is a conserved regulatory kinase gene and a central component of the JNK signaling cascade with key functions during cellular differentiation. It shows complex transcription patterns, and different transcript isoforms are known in the mouse (Mus musculus). We have previously identified a newly evolved testis-specific transcript for the Map2k7 gene in the subspecies M. m. domesticus. Here, we identify the new promoter that drives this transcript and find that it codes for an open reading frame (ORF) of 50 amino acids. The new promoter was gained in the stem lineage of closely related mouse species but was secondarily lost in the subspecies M. m. musculus and M. m. castaneus. A single mutation can be correlated with its transcriptional activity in M. m. domesticus, and cell culture assays demonstrate the capability of this mutation to drive expression. A mouse knockout line in which the promoter region of the new transcript is deleted reveals a functional contribution of the newly evolved promoter to sperm motility and the spermatid transcriptome. Our data show that a new functional transcript (and possibly protein) can evolve within an otherwise highly conserved gene, supporting the notion of regulatory changes contributing to the emergence of evolutionary novelties.

2021 ◽  
Author(s):  
Tobias Heinen ◽  
Chen Xie ◽  
Maryam Keshavarz ◽  
Dominik Stappert ◽  
Sven Kuenzel ◽  
...  

Map2k7 (synonym Mkk7) is a conserved regulatory kinase gene and a central component of the JNK signaling cascade with key functions during cellular differentiation. It shows complex transcription patterns and different transcript isoforms are known in the mouse (Mus musculus). We have previously identified a newly evolved testis specific transcript for the Map2k7 gene in the subspecies M. m. domesticus. Here, we identify the new promotor that drives this transcript and find that its transcript codes for an open reading frame (ORF) of 50 amino acids. The new promotor was gained in the stem lineage of closely related mouse species, but was secondarily lost in the subspecies M. m. musculus and M. m. castaneus. A single mutation can be correlated with its transcriptional activity in M. m. domesticus and cell culture assays demonstrate the capability of this mutation to drive expression. A mouse knock-out line in which the promotor region of the new transcript is deleted reveals a functional contribution of the newly evolved promotor to sperm motility and to the spermatid transcriptome. Our data show that a new functional transcript (and possibly protein) can evolve within an otherwise highly conserved gene, supporting the notion of regulatory changes contributing to the emergence of evolutionary novelties.


2000 ◽  
Vol 14 (5) ◽  
pp. 604-614
Author(s):  
Rafael Fernandez ◽  
Fumitaka Takahashi ◽  
Zhao Liu ◽  
Ruth Steward ◽  
David Stein ◽  
...  

Dorsal closure (DC) in the Drosophila embryo requires the coordinated interaction of two different functional domains of the epidermal cell layer—the leading edge (LE) and the lateral epidermis. In response to activation of a conserved c-Jun amino-terminal kinase (JNK) signaling module, the dorsal-most layer of cells, which constitute the LE of the stretching epithelial sheet, secrete Dpp, a member of the TGFβ superfamily. Dpp and other LE cell-derived signaling molecules stimulate the bilateral dorsal elongation of cells of the dorsolateral epidermis over the underlaying amnioserosa and the eventual fusion of their LEs along the dorsal midline. We have found that flies bearing a Shark tyrosine kinase gene mutation,shark1, exhibit a DC-defective phenotype. Dpp fails to be expressed in shark1 mutant LE cells. Consistent with these observations, epidermal-specific reconstitution ofshark function or overexpression of an activated form of c-Jun in the shark1 mutant background, rescues the DC defect. Thus, Shark regulates the JNK signaling pathway leading to Dpp expression in LE cells. Furthermore, constitutive activation of the Dpp pathway throughout the epidermis fails to rescue theshark1 DC defect, suggesting that Shark may function in additional pathways in the LE and/or lateral epithelium.


2008 ◽  
Vol 89 (3) ◽  
pp. 766-774 ◽  
Author(s):  
Jun-Qing Ge ◽  
Zhang-Nv Yang ◽  
Xu-Dong Tang ◽  
Hai-Jun Xu ◽  
Jian Hong ◽  
...  

Open reading frame (ORF) 67 (Bm67) of the Bombyx mori nucleopolyhedrovirus (BmNPV) is a highly conserved gene that is found in all completely sequenced baculoviruses; its function is unknown. In the present study, a Bm67-knockout virus was generated for studying the role of Bm67 in the BmNPV infection cycle. Furthermore, a Bm67-repair bacmid was constructed by transposing the Bm67 native promoter-promoted Bm67 ORF into the polyhedrin locus of the Bm67-knockout bacmid. After these recombinant bacmids were transfected into BmN cells, the Bm67-knockout bacmid caused defects in the production of infectious budded viruses. However, the Bm67-repair bacmid could rescue the defect, and budded virus titres reached wild-type levels. Quantitative real-time PCR analysis indicated that Bm67 is required for normal levels of DNA synthesis or for the stability of nascent viral DNA at the early stage. Electron microscopic analysis revealed that the formation of normal-appearing nucleocapsids is reduced in Bm67-knockout bacmid-transfected cells, and nucleocapsids are rarely found in the cytoplasm. The presence of ‘enveloped’ nucleocapsids at the nucleoplasm bilayer indicated that they are enveloped abnormally. These results indicated that Bm67 is required for the production of infectious budded viruses and for assembly of envelope and nucleocapsids.


2006 ◽  
Vol 19 (4) ◽  
pp. 389-398 ◽  
Author(s):  
Rahim Mehrabi ◽  
Theo van der Lee ◽  
Cees Waalwijk ◽  
Gert H. J. Kema

Among expressed sequence tag libraries of Mycosphaerella graminicola isolate IPO323, we identified a full-length cDNA clone with high homology to the mitogen-activated protein (MAP) kinase Slt2 in Saccharomyces cerevisiae. This MAP kinase consists of a 1,242-bp open reading frame, and encodes a 414-amino-acid protein. We designated this homolog MgSlt2, generated MgSlt2 knockout strains in M. graminicola isolate IPO323, and found several altered phenotypes in vitro as well as in planta. In yeast glucose broth, MgSlt2 disruptants showed a defective polarized growth in the tip cells upon aging, causing substantial local enlargements culminating in large swollen cells containing two to four nuclei. The MgSlt2 disruptants showed a significantly increased sensitivity to several fungicides, including miconazole (2×), bifonazole (>4×), imazalil (5×), and cyproconazole (10×), and were hypersensitive to glucanase. Unlike the wild type, MgSlt2 disruptants did not produce aerial mycelia and did not melanize on potato dextrose agar. Although cytological analysis in planta showed normal penetration of wheat stomata by the germ tubes of the MgSlt2 disruptants, subsequently formed hyphal filaments frequently were unable to branch out and establish invasive growth resulting in highly reduced virulence, and prevented pycnidia formation. Therefore, we conclude that MgSlt2 is a new pathogenicity factor in M. graminicola.


2020 ◽  
Vol 48 (17) ◽  
pp. 9724-9746
Author(s):  
Ravi K Patel ◽  
Jessica D West ◽  
Ya Jiang ◽  
Elizabeth A Fogarty ◽  
Andrew Grimson

Abstract The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1209-1209
Author(s):  
Xueqin Sun ◽  
Bin Lu ◽  
Zan Huang

Abstract Phorbol 12-myristate 13-acetate (TPA) primarily activates PKC and subsequently leads to activation of downstream signaling pathways including MAPK/ERK, SAPK/JNK, and NF-κB, which causes gene expression alteration and leukemic cell differentiation. How these TPA-induced genes may contribute to leukemic cell differentiation remains to be addressed. We noticed that a novel gene chromosome 7 open reading frame 41 (C7ORF41) was one of TPA-induced genes without any known functions. Differential expression of C7ORF41 has been identified in human embryo development and predicted to function in hematopoiesis based on hierarchical clustering analysis. To support this, we found high expression level of C7ORF41 in bone marrow. By using K562 cell as a model, we discovered that ectopic expression of C7ORF41 significantly promoted TPA-induced megakaryocyte differentiation evidenced by an increase of CD61 expression. Consistently, two types of transcription factors critical for megakaryopoiesis, RUNX1 and ETS proteins, were simultaneously upregulated by C7ORF41. Furthermore, cytoplasmic distribution of C7ORF41 suggests that it may act as a signaling molecule. As expected, C7ORF41 overexpression enhanced ERK and JNK phosphorylation. In contrast, C7ORF41 knockdown led to an opposite phenotype: impaired megakaryocyte differentiation, attenuated signaling, and reduced transcription factor expression. These observations suggest that C7ORF41 may promote megakaryocyte differentiation by enhancing ERK and JNK signaling that subsequently leads to upregulation of RUNX1 and ETS proteins. Indeed, C7ORF41 overexpression rescued megakaryocyte differentiation blocked by PD98059, a potent ERK inhibitor, while JNK inhibition abrogated the effect of C7ORF41 on upregulation of ETS proteins. In addition, C7ORF41 was highly conserved in evolution and several tyrosine residues including Y34 were strictly preserved, suggesting the importance of tyrosine phosphorylation in C7ORF41 function. In fact, mutant C7ORF41 with Y34 substitution by phenylalanine functioned to inhibit megakaryocyte differentiation. Finally, NF-κB appeared to be the major activator of C7ORF41 that in turn repressed NF-κB activity by inhibiting its phosphorylation at serine 536. Taken together, we have identified novel function of a new gene C7ORF41 that may promote leukemic megakaryocyte differentiation through a novel mechanism in which C7ORF41 forms a well-balanced regulatory network in TPA-induced signaling. In this network, initial TPA treatment primes downstream signaling including MAPK/ERK, SAPK/JNK, and NF-kB. TPA-induced NF-κB activation further upregulates C7ORF41 that may serve to amplify TPA-induced ERK and JNK signaling to ensure megakaryocyte differentiation. On the other hand, C7ORF41 upregulation also serves as a negative regulator of NF-κB activity that may quench TPA-indcued NF-κB signaling. In addition, enhanced ERK signaling feeds back to damp C7ORF41 upregulation that may tune TPA-induced signaling under controllable level. Our findings shed light on understanding forced differentiation in leukemic cells and may provide useful information for rational differentiation therapy. Disclosures: No relevant conflicts of interest to declare.


2000 ◽  
Vol 44 (3) ◽  
pp. 787-789 ◽  
Author(s):  
C. A. Franke ◽  
T. M. Bolman ◽  
S. A. Ottum ◽  
K. F. Jones ◽  
D. E. Hruby

ABSTRACT Mutants of Streptococcus gordonii resistant to 5-fluorodeoxyuridine (FUdRr) were isolated. Each strain contained a point mutation resulting in the premature termination of the thymidine kinase (TK) open reading frame (tdk). In vitro translation of the mutant tdkcoding regions resulted in synthesis of truncated TK polypeptides deficient in TK activity.


1989 ◽  
Vol 9 (4) ◽  
pp. 1587-1593
Author(s):  
Q L Hao ◽  
N Heisterkamp ◽  
J Groffen

Using v-abl probes, we have identified and cloned a novel fes/fps-homologous human cDNA, which we have designated FER (pronounced "fair"). This apparently full-length cDNA of 3.0 kilobases has an open reading frame of 2,466 base pairs and the capacity to encode a protein of 94,000 molecular weight. The cDNA contains regions homologous to the highly conserved tyrosine protein kinase domain of other oncogenes and growth factor receptors but lacks a clear transmembrane region, indicating that it encodes a tyrosine kinase of the nonreceptor type. The deduced amino acid sequence of FER resembles that of c-fes/fps. Our data indicate that the protein product of FER, p94FER, corresponds to a previously reported cellular phosphoprotein, NCP94, detected with a v-fps-specific antipeptide antiserum.


2007 ◽  
Vol 81 (6) ◽  
pp. 3018-3026 ◽  
Author(s):  
Y. W. Huang ◽  
T. Opriessnig ◽  
P. G. Halbur ◽  
X. J. Meng

ABSTRACT To determine the initiation strategy of the hepatitis E virus (HEV) open reading frame 3 (ORF3), we constructed five HEV mutants with desired mutations in the ORF1 and ORF2 junction region and tested their levels of in vivo infectivity in pigs. A mutant with a C-terminally truncated ORF3 is noninfectious in pigs, indicating that an intact ORF3 is required for in vivo infectivity. Mutations with substitutions in the first in-frame AUG in the junction region or with the same T insertion at the corresponding position of HEV genotype 4 did not affect the virus infectivity or rescue, although mutations with combinations of the two affected virus recovery efficiency, and a single mutation at the third in-frame AUG completely abolished virus infectivity in vivo, indicating that the third in-frame AUG in the junction region is required for virus infection and is likely the authentic initiation site for ORF3. A conserved double stem-loop RNA structure, which may be important for HEV replication, was identified in the junction region. This represents the first report of using a unique homologous pig model system to study the molecular mechanism of HEV replication and to systematically and definitively identify the authentic ORF3 initiation site.


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