Structural elements of the ubiquitin-independent proteasome degron of ornithine decarboxylase

2008 ◽  
Vol 410 (2) ◽  
pp. 401-407 ◽  
Author(s):  
Junko Takeuchi ◽  
Hui Chen ◽  
Martin A. Hoyt ◽  
Philip Coffino

Mouse ODC (ornithine decarboxylase) is quickly degraded by the 26S proteasome in mammalian and fungal cells. Its degradation is independent of ubiquitin but requires a degradation signal composed of residues 425–461 at the ODC C-terminus, cODC (the last 37 amino acids of the ODC C-terminus). Mutational analysis of cODC revealed the presence of two essential elements in the degradation signal. The first consists of cysteine and alanine at residues 441 and 442 respectively. The second element is the C-terminus distal to residue 442; it has little or no sequence specificity, but is intolerant of insertions or deletions that alter its span. Reducing conditions, which preclude all well-characterized chemical reactions of the Cys441 thiol, are essential for in vitro degradation. These experiments imply that the degradative function of Cys441 does not involve its participation in chemical reaction; it, instead, functions within a structural element for recognition by the 26S proteasome.

2005 ◽  
Vol 83 (4) ◽  
pp. 497-504 ◽  
Author(s):  
Benoit Coulombe ◽  
Marie-France Langelier

High resolution X-ray crystal structures of multisubunit RNA polymerases (RNAP) have contributed to our understanding of transcriptional mechanisms. They also provided a powerful guide for the design of experiments aimed at further characterizing the molecular stages of the transcription reaction. Our laboratory used tandem-affinity peptide purification in native conditions to isolate human RNAP II variants that had site-specific mutations in structural elements located strategically within the enzyme's catalytic center. Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme.Key words: RNA polymerase II, transcriptional mechanisms, mutational analysis, mRNA synthesis.


2020 ◽  
Vol 202 (23) ◽  
Author(s):  
Anastasiia N. Klimova ◽  
Steven J. Sandler

ABSTRACT Escherichia coli PriA and PriC recognize abandoned replication forks and direct reloading of the DnaB replicative helicase onto the lagging-strand template coated with single-stranded DNA-binding protein (SSB). Both PriA and PriC have been shown by biochemical and structural studies to physically interact with the C terminus of SSB. In vitro, these interactions trigger remodeling of the SSB on ssDNA. priA341(R697A) and priC351(R155A) negated the SSB remodeling reaction in vitro. Plasmid-carried priC351(R155A) did not complement priC303::kan, and priA341(R697A) has not yet been tested for complementation. Here, we further studied the SSB-binding pockets of PriA and PriC by placing priA341(R697A), priA344(R697E), priA345(Q701E), and priC351(R155A) on the chromosome and characterizing the mutant strains. All three priA mutants behaved like the wild type. In a ΔpriB strain, the mutations caused modest increases in SOS expression, cell size, and defects in nucleoid partitioning (Par−). Overproduction of SSB partially suppressed these phenotypes for priA341(R697A) and priA344(R697E). The priC351(R155A) mutant behaved as expected: there was no phenotype in a single mutant, and there were severe growth defects when this mutation was combined with ΔpriB. Analysis of the priBC mutant revealed two populations of cells: those with wild-type phenotypes and those that were extremely filamentous and Par− and had high SOS expression. We conclude that in vivo, priC351(R155A) identified an essential residue and function for PriC, that PriA R697 and Q701 are important only in the absence of PriB, and that this region of the protein may have a complicated relationship with SSB. IMPORTANCE Escherichia coli PriA and PriC recruit the replication machinery to a collapsed replication fork after it is repaired and needs to be restarted. In vitro studies suggest that the C terminus of SSB interacts with certain residues in PriA and PriC to recruit those proteins to the repaired fork, where they help remodel it for restart. Here, we placed those mutations on the chromosome and tested the effect of mutating these residues in vivo. The priC mutation completely abolished function. The priA mutations had no effect by themselves. They did, however, display modest phenotypes in a priB-null strain. These phenotypes were partially suppressed by SSB overproduction. These studies give us further insight into the reactions needed for replication restart.


2002 ◽  
Vol 184 (15) ◽  
pp. 4148-4160 ◽  
Author(s):  
Igor N. Olekhnovich ◽  
Robert J. Kadner

ABSTRACT The HilC and HilD proteins of Salmonella enterica serovar Typhimurium are members of the AraC/XylS family of transcription regulators. They are encoded on Salmonella pathogenicity island 1 (SPI1) and control expression of the hilA gene, which encodes the major transcriptional activator for many genes encoded on SPI1 and elsewhere that contribute to invasion of host cells. Gel electrophoretic shift and DNase footprinting assays revealed that purified HilC and HilD proteins can bind to multiple regions in the hilA and hilC promoters and to a single region in the hilD promoter. Although both HilC and -D proteins can bind to the same DNA regions, they showed different dependencies on the sequence and lengths of their DNA targets. To identify the binding-sequence specificity of HilC and HilD, a series of single base substitutions changing each position in a DNA fragment corresponding to positions −92 to −52 of the hilC promoter was tested for binding to HilC and HilD in a gel shift DNA-binding assay. This mutational analysis in combination with sequence alignments allowed deduction of consensus sequences for binding of both proteins. The consensus sequences overlap but differ so that HilC can bind to both types of sites but HilD only to one. The hilA and hilC promoters contain multiple binding sites of each type, whereas the hilD promoter contains a site that binds HilC but not HilD without additional binding elements. The HilC and HilD proteins had no major effect on transcription from the hilA or hilD promoters using purified proteins in vitro but changed the choice of promoter at hilC. These results are consistent with a model derived from analysis of lacZ fusions stating that HilC and HilD enhance hilA expression by counteracting a repressing activity.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2853-2853
Author(s):  
Linsheng Zhang ◽  
Jenice D’Costa ◽  
Tanawan Kummalue ◽  
Isabel Moreno ◽  
Curt I. Civin ◽  
...  

Abstract CBFβ complexes with RUNX1/AML1 to form Core Binding Factor. CBFβ-SMMHC is expressed from the inv(16) or t(16;16) chromosome in 8% of AML cases. This fusion protein contains the majority of CBFβ linked to the α-helical rod domain of smooth muscle myosin heavy chain. CBFβ-SMMHC is thought to contribute to leukemogensis by dominantly inhibiting RUNX1/AML1. Inhibition of AML1 depends upon the integrity of a 28 amino acid region near the C-terminus of the SMMHC segment termed the Assembly Competence Domain (ACD). A homologous region is present in multiple myosins and is required for optimal multimerization of their respective rod domains. The ACD is located within a 63 residue "extended" ACD, which includes 12 residues N-terminal and 23 residues C-terminal to the ACD. The extended ACD was noted to have a more neutral charge than other segments of myosin rods. We have now carried out a mutagenic analysis of individual α-helices within or near the extended ACD and have assessed the effect of these mutations on the ability of CBFβ-SMMHC to multimerize in vitro and to inhibit endogenous AML1 activities in the Ba/F3 cell line and in normal murine myeloid progenitors. The 7 amino acids constituting a single turn of the rod domain α-helix are designated abcdefg. The a and d residues form a hydrophobic surface that mediates coiled-coil dimerization, the e and g residues often form salt bridges that stabilize the dimer, and the b, c and f residues are on the outer surface of the helix and are the best candidates for mediating multimerization. We have therefore mutated the bcf residues as a group in ten helices, N3, N1, A, B, C, D, E, F, G, and H. A–D constitutes the core, 28 residue ACD. N3 and N1 are three or one helix N-terminal to helix A. Mutation of N3 or N1 did not affect multimerization in low ionic strength or the ability of CBFβ-SMMHC to inhibit AML1-mediated G1 to S cell cycle progression in Ba/F3 cells. In contrast, mutation of helices A, B, C, D, E, F, G, or H both impaired multimerization in vitro and prevented cell cycle slowing in Ba/F3 cells. Mutants A–E are each located predominantly in the cell nucleus. In transduced murine myeloid progenitors, mutant N3 again behaved similar to intact CBFβ-SMMHC, mutant A also markedly slowed proliferation, mutant B had an intermediate effect, and mutants C, D, or E did not slow proliferation, each in three independent experiments. The increased activities of mutants A or B in the latter setting may reflect the fact that Ba/F3 cells accumulate three times faster than myeloid progenitors and so perhaps are more sensitive to subtle effects. Sin3A, a co-repressor shown to interact with CBFβ-SMMHC, retained the ability to bind mutants A–E. Analysis of mutants N1 and F–H for mSin3A binding, nuclear localization, and their effects on normal progenitor proliferation is in progress. Together, these findings indicate that a surface near the C-terminus of the CBFβ-SMMHC rod domain, encompassing much of the "extended ACD", is required for multimerization and inhibition of AML1. Helices N1 and H demarcate the boundaries of this surface, with helix H been the very last helix of the rod domain. Further characterization of the molecular interactions which allow this surface to mediate SMMHC multimerization may enable the rationale design of drugs for the therapy of AML associated with inv(16).


1993 ◽  
Vol 13 (12) ◽  
pp. 7864-7873 ◽  
Author(s):  
B K Haarer ◽  
A S Petzold ◽  
S S Brown

We have mutated two regions within the yeast profilin gene in an effort to functionally dissect the roles of actin and phosphatidylinositol 4,5-bisphosphate (PIP2) binding in profilin function. A series of truncations was carried out at the C terminus of profilin, a region that has been implicated in actin binding. Removal of the last three amino acids nearly eliminated the ability of profilin to bind polyproline in vitro but had no dramatic in vivo effects. Thus, the extreme C terminus is implicated in polyproline binding, but the physiological relevance of this interaction is called into question. More extensive truncation, of up to eight amino acids, had in vivo effects of increasing severity and resulted in changes in conformation and expression level of the mutant profilins. However, the ability of these mutants to bind actin in vitro was not eliminated, suggesting that this region cannot be solely responsible for actin binding. We also mutagenized a region of profilin that we hypothesized might be involved in PIP2 binding. Alteration of basic amino acids in this region produced mutant profilins that functioned well in vivo. Many of these mutants, however, were unable to suppress the loss of adenylate cyclase-associated protein (Cap/Srv2p [A. Vojtek, B. Haarer, J. Field, J. Gerst, T. D. Pollard, S. S. Brown, and M. Wigler, Cell 66:497-505, 1991]), indicating that a defect could be demonstrated in vivo. In vitro assays demonstrated that the inability to suppress loss of Cap/Srv2p correlated with a defect in the interaction with actin, independently of whether PIP2 binding was reduced. Since our earlier studies of Acanthamoeba profilins suggested the importance of PIP2 binding for suppression, we conclude that both activities are implicated and that an interplay between PIP2 binding and actin binding may be important for profilin function.


Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 864
Author(s):  
Ju-Yi Hsieh ◽  
Yen-Chin Liu ◽  
I-Ting Cheng ◽  
Chu-Ju Lee ◽  
Yu-Hsuan Wang ◽  
...  

Antizyme (AZ) is a protein that negatively regulates ornithine decarboxylase (ODC). AZ achieves this inhibition by binding to ODC to produce AZ-ODC heterodimers, abolishing enzyme activity and targeting ODC for degradation by the 26S proteasome. In this study, we focused on the biomolecular interactions between the C-terminal domain of AZ (AZ95–228) and ODC to identify the functional elements of AZ that are essential for binding, inhibiting and degrading ODC, and we also identified the crucial factors governing the differential binding and inhibition ability of AZ isoforms toward ODC. Based on the ODC inhibition and AZ-ODC binding studies, we demonstrated that amino acid residues reside within the α1 helix, β5 and β6 strands, and connecting loop between β6 and α2 (residues 142–178), which is the posterior part of AZ95–228, play crucial roles in ODC binding and inhibition. We also identified the essential elements determining the ODC-degradative activity of AZ; amino acid residues within the anterior part of AZ95–228 (residues 120–145) play crucial roles in AZ-mediated ODC degradation. Finally, we identified the crucial factors that govern the differential binding and inhibition of AZ isoforms toward ODC. Mutagenesis studies of AZ1 and AZ3 and their binding and inhibition revealed that the divergence of amino acid residues 124, 150, 166, 171, and 179 results in the differential abilities of AZ1 and AZ3 in the binding and inhibition of ODC.


1994 ◽  
Vol 14 (1) ◽  
pp. 87-92 ◽  
Author(s):  
X Li ◽  
P Coffino

Selective degradation by proteasomes of ornithine decarboxylase, the initial enzyme in polyamine biosynthesis, is mediated by the polyamine-inducible protein antizyme. Antizyme binds to a region near the N terminus of ornithine decarboxylase (X. Li and P. Coffino, Mol. Cell. Biol. 12:3556-3562, 1992). This interaction induces a conformational change in ornithine decarboxylase that exposes its C terminus and inactivates the enzyme (X. Li and P. Coffino, Mol. Cell. Biol. 13:1487-1492, 1993). Here we show that the C-terminal half of antizyme alone can inactivate ornithine decarboxylase and alter its conformation, but it cannot direct degradation of the enzyme, either in vitro or in vivo. A portion of the N-terminal half of antizyme must be present to promote degradation.


2020 ◽  
Vol 219 (12) ◽  
Author(s):  
Andrea Serra-Marques ◽  
Ronja Houtekamer ◽  
Dorine Hintzen ◽  
John T. Canty ◽  
Ahmet Yildiz ◽  
...  

Eukaryotic cells typically form a single, round nucleus after mitosis, and failures to do so can compromise genomic integrity. How mammalian cells form such a nucleus remains incompletely understood. NuMA is a spindle protein whose disruption results in nuclear fragmentation. What role NuMA plays in nuclear integrity, and whether its perceived role stems from its spindle function, are unclear. Here, we use live imaging to demonstrate that NuMA plays a spindle-independent role in forming a single, round nucleus. NuMA keeps the decondensing chromosome mass compact at mitotic exit and promotes a mechanically robust nucleus. NuMA’s C terminus binds DNA in vitro and chromosomes in interphase, while its coiled-coil acts as a central regulatory and structural element: it prevents NuMA from binding chromosomes at mitosis, regulates its nuclear mobility, and is essential for nuclear formation. Thus, NuMA plays a structural role over the cell cycle, building and maintaining the spindle and nucleus, two of the cell’s largest structures.


1996 ◽  
Vol 16 (11) ◽  
pp. 6200-6207 ◽  
Author(s):  
V Prapapanich ◽  
S Chen ◽  
E J Toran ◽  
R A Rimerman ◽  
D F Smith

The hsp70-interacting protein Hip participates in the assembly pathway for progesterone receptor complexes. During assembly, Hip appears at early assembly stages in a transient manner that parallels hsp70 interactions. In this study, a cDNA for human Hip was used to develop various mutant Hip forms in the initial mapping of functions to particular Hip structural elements. Hip regions targeted for deletion and/or truncation included the C-terminal region (which has some limited homology with Saccharomyces cerevisiae Sti1 and its vertebrate homolog p60), a glycine-glycine-methionine-proline (GGMP) tandem repeat, and a tetratricopeptide repeat (TPR). Binding of Hip to hsp70's ATPase domain was lost with deletions from the TPR and from an adjoining highly charged region; correspondingly, these Hip mutant forms were not recovered in receptor complexes. Truncation of Hip's Sti1-related C terminus resulted in Hip binding to hsp70 in a manner suggestive of a misfolded peptide substrate; this hsp70 binding was localized to the GGMP tandem repeat. Mutants lacking either the C terminus or the GGMP tandem repeat were still recovered in receptor complexes. Truncations from Hip's N terminus resulted in an apparent loss of Hip homo-oligomerization, but these mutants retained association with hsp70 and were recovered in receptor complexes. This mutational analysis indicates that Hip's TPR is required for binding of Hip with hsp70's ATPase domain. In addition, some data suggest that hsp70's peptide-binding domain may alternately or concomitantly bind to Hip's GGMP repeat in a manner regulated by Sti1-related sequences.


2010 ◽  
Vol 189 (7) ◽  
pp. 1143-1155 ◽  
Author(s):  
Christopher W. Carroll ◽  
Kirstin J. Milks ◽  
Aaron F. Straight

Centromeres contain specialized nucleosomes in which histone H3 is replaced by the histone variant centromere protein A (CENP-A). CENP-A nucleosomes are thought to act as an epigenetic mark that specifies centromere identity. We previously identified CENP-N as a CENP-A nucleosome-specific binding protein. Here, we show that CENP-C also binds directly and specifically to CENP-A nucleosomes. Nucleosome binding by CENP-C required the extreme C terminus of CENP-A and did not compete with CENP-N binding, which suggests that CENP-C and CENP-N recognize distinct structural elements of CENP-A nucleosomes. A mutation that disrupted CENP-C binding to CENP-A nucleosomes in vitro caused defects in CENP-C targeting to centromeres. Moreover, depletion of CENP-C with siRNA resulted in the mislocalization of all other nonhistone CENPs examined, including CENP-K, CENP-H, CENP-I, and CENP-T, and led to a partial reduction in centromeric CENP-A. We propose that CENP-C binds directly to CENP-A chromatin and, together with CENP-N, provides the foundation upon which other centromere and kinetochore proteins are assembled.


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