scholarly journals Codon bias determines sorting of ion channel protein

2020 ◽  
Author(s):  
Marina Kithil ◽  
Anja Jeannine Engel ◽  
Markus Langhans ◽  
Oliver Rauh ◽  
Matea Cartolano ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Secretory Pathway ◽  
Model Systems ◽  
Dependent Manner ◽  
Intracellular Proteins ◽  
Polypeptide Folding ◽  
A Cell ◽  
Identical Amino Acid Sequence ◽  
Cycle Dependent ◽  
The Impact

AbstractThe choice of codons can influence local translation kinetics during protein synthesis. The question of whether the modulation of polypeptide folding and binding to chaperons influences sorting of nascent membrane proteins remains unclear. Here, we use two similar K+ channels as model systems to examine the impact of codon choice on protein sorting. By monitoring transient expression of GFP tagged proteins in mammalian cells we find that targeting of one channel to the secretory pathway is insensitive to codon optimization. In contrast, sorting of the second channel to the mitochondria is very sensitive to codon choice. The protein with an identical amino acid sequence is sorted in a codon and cell cycle dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves together with a cell-state depending decoding mechanism as a secondary code for sorting intracellular proteins.

scholarly journals Codon Bias Can Determine Sorting of a Potassium Channel Protein

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1128
Author(s):  
Anja J. Engel ◽  
Marina Kithil ◽  
Markus Langhans ◽  
Oliver Rauh ◽  
Matea Cartolano ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Codon Bias ◽  
Secretory Pathway ◽  
Model Systems ◽  
Dependent Manner ◽  
Intracellular Membrane ◽  
Synonymous Codons ◽  
State Dependent ◽  
A Cell ◽  
Cycle Dependent

Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K+ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves, together with a cell-state-dependent decoding mechanism, as a secondary code for sorting intracellular membrane proteins.

Regulation of the expression and activity of Unr in mammalian cells

2015 ◽  
Vol 43 (6) ◽  
pp. 1241-1246 ◽  
Author(s):  
Emma C. Anderson ◽  
Pól Ó Catnaigh
Keyword(s):  
Mammalian Cells ◽  
Alternative Polyadenylation ◽  
Dependent Manner ◽  
Factor X ◽  
Mammalian Development ◽  
Ras Gene ◽  
Polypyrimidine Tract Binding Protein ◽  
A Cell ◽  
Internal Initiation ◽  
Cycle Dependent

Unr (upstream of N-ras) is a post-transcriptional regulator of gene expression, essential for mammalian development and mutated in many human cancers. The expression of unr is itself regulated at many levels; transcription of unr, which also affects expression of the downstream N-ras gene, is tissue and developmental stage-dependent and is repressed by c-Myc and Max (Myc associated factor X). Alternative splicing gives rise to six transcript variants, which include three different 5′-UTRs. The transcripts are further diversified by the use of three alternative polyadenylation signals, which governs whether AU-rich instability elements are present in the 3′-UTR or not. Translation of at least some unr transcripts can occur by internal initiation and is regulated in a cell-cycle-dependent manner; binding of PTB (polypyrimidine tract-binding protein) and Unr to the 5′-UTR inhibits translation, but these are displaced by heterogeneous nuclear ribonucleoproteins C1/C2 (hnRNPC1/C2) during mitosis to stimulate translation. Finally, Unr is post-translationally modified by phosphorylation and lysine acetylation, although it is not yet known how these modifications affect Unr activity.

scholarly journals Molecular Signals in the Trafficking of Toxoplasma gondii Protein MIC3 to the Micronemes

2008 ◽  
Vol 7 (6) ◽  
pp. 1019-1028 ◽  
Author(s):  
Hiba El Hajj ◽  
Julien Papoin ◽  
Odile Cérède ◽  
Nathalie Garcia-Réguet ◽  
Martine Soête ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Secretory Pathway ◽  
Protozoan Parasite ◽  
Dependent Manner ◽  
Dense Granules ◽  
Golgi Compartment ◽  
A Cell ◽  
Epidermal Growth ◽  
Cycle Dependent ◽  
Molecular Signals

ABSTRACT The protozoan parasite Toxoplasma gondii is equipped with a sophisticated secretory apparatus, including three distinct exocytic organelles, named micronemes, rhoptries, and dense granules. We have dissected the requirements for targeting the microneme protein MIC3, a key component of T. gondii infection. We have shown that MIC3 is processed in a post-Golgi compartment and that the MIC3 propeptide and epidermal growth factor (EGF) modules contain microneme-targeting information. The minimal requirement for microneme delivery is defined by the propeptide plus any one of the three EGF domains. We have demonstrated that the cleavage of the propeptide, the dimerization of MIC3, and the chitin binding-like sequence, which are crucial for host cell binding and virulence, are dispensable for proper targeting. Finally, we have shown that part of MIC3 is withheld in the secretory pathway in a cell cycle-dependent manner.

scholarly journals Poly ADP-ribosylation of SET8 leads to aberrant H4K20me1 domains in mammalian cells

2021 ◽  
Author(s):  
Pierre-Olivier Esteve ◽  
Vishnu Udayakumaran Nair Sunitha Kumary ◽  
Christian Ruse ◽  
Hang Gyeong Chin ◽  
Sriharsa Pradhan
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Dynamic Equilibrium ◽  
Dependent Manner ◽  
Histone H4 ◽  
Adp Ribosylation ◽  
Genome Wide ◽  
Lysine Residues ◽  
A Cell ◽  
Cycle Dependent

In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in a cell cycle-dependent manner. Poly ADP-ribosylation on SET8 renders it catalytically compromised and it undergoes degradation via ubiquitylation pathway. Knockdown of PARP1 shifted the relative dynamic equilibrium of H4K20me2 to H4k20me3 in cells. Overexpression or knockdown of PARP1 led to aberrant H4K20me1 domains genome-wide, impacting Wnt signaling pathways genes and transcription factor binding site enrichment. Therefore, SET8 mediated chromatin remodeling and gene expression in mammalian cells are influenced by poly ADP-ribosylation by PARP1.

scholarly journals Truncated APC regulates the transcriptional activity of β-catenin in a cell cycle dependent manner

2006 ◽  
Vol 16 (2) ◽  
pp. 199-209 ◽  
Author(s):  
Jean Schneikert ◽  
Annette Grohmann ◽  
Jürgen Behrens
Keyword(s):  
Cell Cycle ◽  
Transcriptional Activity ◽  
Dependent Manner ◽  
A Cell ◽  
Cycle Dependent

Structural models for the self-assembly and microtubule interactions of gamma-, delta- and epsilon-tubulin

2001 ◽  
Vol 114 (2) ◽  
pp. 413-422 ◽  
Author(s):  
Y.F. Inclan ◽  
E. Nogales
Keyword(s):  
Self Assembly ◽  
Structural Models ◽  
Dependent Manner ◽  
Gamma Delta ◽  
Sequence Comparisons ◽  
Alpha Tubulin ◽  
A Cell ◽  
Gamma Tubulin ◽  
Cycle Dependent ◽  
Key Residues

alphabeta-tubulin heterodimers self-assemble to form microtubules nucleated by gamma-tubulin in the cell. Gamma-tubulin is believed to recruit the alphabeta-tubulin dimers that form the minus ends of microtubules, but the molecular mechanism of this action remains a matter of heated controversy. Still less is known about the function and molecular interactions of delta-tubulin and epsilon-tubulin. delta-tubulin may seed the formation of the C triplet tubules in the basal bodies of Chlamydomonas and epsilon-tubulin is known to localize to the centrosome in a cell cycle-dependent manner. Using the structure of alphabeta tubulin as a model, we have analyzed the sequences of gamma-, delta- and epsilon-tubulin in regions corresponding to different polymerization interfaces in the tubulin alphabeta dimer. The sequence comparisons sometimes show clear conservation, pointing to similar types of contacts being functionally important for the new tubulin considered. Conversely, certain surfaces show marked differences that rule out equivalent interactions for non-microtubular tubulins. This sequence/structure analysis has led us to structural models of how these special tubulins may be involved in protein-protein contacts that affect microtubule self-assembly. delta-tubulin most likely interacts longitudinally with alpha-tubulin at the minus ends of microtubules, while epsilon-tubulin most likely binds to the plus end of beta-tubulin. Conservation of key residues in gamma-tubulin suggests that it is capable of longitudinal self-assembly. The implications for the protofilament and template models of nucleation are considered.

scholarly journals E2F activity is regulated by cell cycle-dependent changes in subcellular localization.

1997 ◽  
Vol 17 (12) ◽  
pp. 7268-7282 ◽  
Author(s):  
R Verona ◽  
K Moberg ◽  
S Estes ◽  
M Starz ◽  
J P Vernon ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Subcellular Localization ◽  
Nuclear Localization ◽  
Mammalian Cells ◽  
Critical Role ◽  
Biological Properties ◽  
Dependent Manner ◽  
Restriction Point ◽  
Cycle Dependent ◽  
Almost All

E2F directs the cell cycle-dependent expression of genes that induce or regulate the cell division process. In mammalian cells, this transcriptional activity arises from the combined properties of multiple E2F-DP heterodimers. In this study, we show that the transcriptional potential of individual E2F species is dependent upon their nuclear localization. This is a constitutive property of E2F-1, -2, and -3, whereas the nuclear localization of E2F-4 is dependent upon its association with other nuclear factors. We previously showed that E2F-4 accounts for the majority of endogenous E2F species. We now show that the subcellular localization of E2F-4 is regulated in a cell cycle-dependent manner that results in the differential compartmentalization of the various E2F complexes. Consequently, in cycling cells, the majority of the p107-E2F, p130-E2F, and free E2F complexes remain in the cytoplasm. In contrast, almost all of the nuclear E2F activity is generated by pRB-E2F. This complex is present at high levels during G1 but disappears once the cells have passed the restriction point. Surprisingly, dissociation of this complex causes little increase in the levels of nuclear free E2F activity. This observation suggests that the repressive properties of the pRB-E2F complex play a critical role in establishing the temporal regulation of E2F-responsive genes. How the differential subcellular localization of pRB, p107, and p130 contributes to their different biological properties is also discussed.

scholarly journals Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice

2021 ◽  
Author(s):  
Yuting Liu ◽  
Kehui Wang ◽  
Li Huang ◽  
Jicheng Zhao ◽  
Xinpeng Chen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Viability ◽  
Histone H3 ◽  
Dependent Manner ◽  
Centromere Function ◽  
Histone H3 Variant ◽  
A Cell ◽  
Cycle Dependent ◽  
Spatiotemporal Control

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.

scholarly journals Gcn5-mediated acetylation at MBF-regulated promoters induces the G1/S transcriptional wave

2019 ◽  
Vol 47 (16) ◽  
pp. 8439-8451 ◽  
Author(s):  
Alberto González-Medina ◽  
Elena Hidalgo ◽  
José Ayté
Keyword(s):  
Cell Cycle ◽  
Molecular Mechanisms ◽  
Histone H3 ◽  
Dependent Manner ◽  
Saga Complex ◽  
Lysine Residues ◽  
Physical Barriers ◽  
A Cell ◽  
Cycle Dependent ◽  
Regulated Promoters

Abstract In fission yeast, MBF-dependent transcription is inactivated at the end of S phase through a negative feedback loop that involves the co-repressors, Yox1 and Nrm1. Although this repression system is well known, the molecular mechanisms involved in MBF activation remain largely unknown. Compacted chromatin constitutes a barrier to activators accessing promoters. Here, we show that chromatin regulation plays a key role in activating MBF-dependent transcription. Gcn5, a part of the SAGA complex, binds to MBF-regulated promoters through the MBF co-activator Rep2 in a cell cycle-dependent manner and in a reverse correlation to the binding of the MBF co-repressors, Nrm1 or Yox1. We propose that the co-repressors function as physical barriers to SAGA recruitment onto MBF promoters. We also show that Gcn5 acetylates specific lysine residues on histone H3 in a cell cycle-regulated manner. Furthermore, either in a gcn5 mutant or in a strain in which histone H3 is kept in an unacetylated form, MBF-dependent transcription is downregulated. In summary, Gcn5 is required for the full activation and correct timing of MBF-regulated gene transcription.

scholarly journals The Epigenetic Repertoire of Daphnia magna Includes Modified Histones

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Nicole F. Robichaud ◽  
Jeanette Sassine ◽  
Margaret J. Beaton ◽  
Vett K. Lloyd
Keyword(s):  
Life Cycle ◽  
Histone H3 ◽  
Dependent Manner ◽  
Nurse Cells ◽  
Important Species ◽  
Clonal Population ◽  
A Cell ◽  
Cycle Dependent

Daphnids are fresh water microcrustaceans, many of which follow a cyclically parthenogenetic life cycle. Daphnia species have been well studied in the context of ecology, toxicology, and evolution, but their epigenetics remain largely unexamined even though sex determination, the production of sexual females and males, and distinct adult morphological phenotypes, are determined epigenetically. Here, we report on the characterization of histone modifications in Daphnia. We show that a number of histone H3 and H4 modifications are present in Daphnia embryos and histone H3 dimethylated at lysine 4 (H3K4me2) is present nonuniformly in the nucleus in a cell cycle-dependent manner. In addition, this histone modification, while present in blastula and gastrula cells as well as the somatic cells of adults, is absent or reduced in oocytes and nurse cells. Thus, the epigenetic repertoire of Daphnia includes modified histones and as these epigenetic forces act on a genetically homogeneous clonal population Daphnia offers an exceptional tool to investigate the mechanism and role of epigenetics in the life cycle and development of an ecologically important species.

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