Monomorphism of human cytochrome c

Bertini, Ivano; Grassi, E.; Luchinat, Claudio; Quattrone, Alessandro; Saccenti, Edoardo

doi:10.1016/j.ygeno.2006.07.010

Cited by 14 publications

(49 citation statements)

References 13 publications

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“…17. TaqMan (Thermo Fisher Scientific) master mix was used for miR-29b-1/a primers (Thermo Fisher Scientific) and SYBR green (QIAGEN) master mix was used for LDHA 57 , ENO1 58 , CYCS 59 , ATP5G1 60 , ATP5C1 61 , ATPIF1 62 , ATP5G3 60 , NDUFS6 63 , NDUFC2 64 . Normalizers included RNU6B or U48 (Thermo Fisher Scientific) for miRNA and GAPDH (SYBR green) 65 and 18S (TaqMan; Thermo Fisher) for mRNA.…”

Section: Methodsmentioning

confidence: 99%

The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells

Muluhngwi

Alizadeh-Rad

Vittitow

et al. 2017

Sci Rep

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Aberrant microRNA expression contributes to breast cancer progression and endocrine resistance. We reported that although tamoxifen stimulated miR-29b-1/a transcription in tamoxifen (TAM)-resistant breast cancer cells, ectopic expression of miR-29b-1/a did not drive TAM-resistance in MCF-7 breast cancer cells. However, miR-29b-1/a overexpression significantly repressed TAM-resistant LCC9 cell proliferation, suggesting that miR-29b-1/a is not mediating TAM resistance but acts as a tumor suppressor in TAM-resistant cells. The target genes mediating this tumor suppressor activity were unknown. Here, we identify miR-29b-1 and miR-29a target transcripts in both MCF-7 and LCC9 cells. We find that miR-29b-1 and miR-29a regulate common and unique transcripts in each cell line. The cellspecific and common downregulated genes were characterized using the MetaCore Gene Ontology (GO) enrichment analysis algorithm. LCC9-sepecific miR-29b-1/a-regulated GO processes include oxidative phosphorylation, ATP metabolism, and apoptosis. Extracellular flux analysis of cells transfected with anti-or pre-miR-29a confirmed that miR-29a inhibits mitochondrial bioenergetics in LCC9 cells. qPCR,luciferase reporter assays, and western blot also verified the ATP synthase subunit genes ATP5G1 and ATPIF1 as bone fide miR29b-1/a targets. Our results suggest that miR-29 repression of TAMresistant breast cancer cell proliferation is mediated in part through repression of genes important in mitochondrial bioenergetics. microRNAs (miRNA, miRs) are 22 nt non-coding RNAs that recognize and bind complementary seed sequences in the 3′-UTR region of a target messenger RNA (mRNA) 1, 2 . This results in translational repression and/or transcriptional degradation of the target gene. By targeting several mRNAs, miRNAs regulate several cellular and biological processes including cell cycle, cell proliferation and cell differentiation, apoptosis, cellular respiration and glycolysis (reviewed in refs 3-6). Aberrant miRNA expression mediates disease initiation and progression in breast and other cancers 7 . Seventy percent of breast tumors express estrogen receptor alpha (ERα) implying eligibility for endocrine therapies including selective estrogen receptor modulators (SERMs), e.g., Tamoxifen (TAM), and aromatase inhibitors (AI), e.g., letrozole. The efficacy of endocrine therapy is limited by relapse in ~40% of patients 8,9 . Endocrine resistance is mediated by multiple mechanisms depending on the type of therapy used (reviewed in refs 10-14). Alterations in miRNA expression are also implicated in endocrine-resistance (reviewed in refs 15 and 16).Previously, we reported miR-29b-1 and miR-29a were downregulated by TAM in TAM-sensitive (TAM-S) MCF-7 BC cells and upregulated in TAM-resistant (TAM-R) LCC2, LCC9, and LY2 BC cells 17 . There are four miR-29 family members in the human genome: miR-29b-2 and miR-29c (chromosome 1q32.2) and miR-29b-1 and miR-29a (chromosome 7q32.3). miR-29b-1 and miR-29a are separated by ~652 bp on the same pri-miRNA transcript [18][1...

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Section: Methodsmentioning

confidence: 99%

The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells

Muluhngwi

Alizadeh-Rad

Vittitow

et al. 2017

Sci Rep

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“…To further investigate the role of the Arg38 sidechain in the peroxidase reaction, we expressed the R38W variant of cytochrome c. This variant was originally reported as a low frequency SNP (rs11548791, p.Arg39Trp, (38)). However it is now unclear if this is a real variant (39), and gnomAD v2.1.1 reports an alternative low frequency SNP (rs1047899818, p.Arg39Gln) (40). Nonetheless, as Trp has a larger van der Waals volume than Arg (0.79 nm 3 compared to 0.59 nm 3 ) and therefore might be expected to block access to substrate, we hypothesized that this variant would decrease the peroxidase activity of cytochrome c. The R38W cytochrome c variant was folded correctly with a hexacoordinate Fe, a slight blue shift of the Soret band, an unchanged Tm, but a lowered redox potential when compared to WT (Table S1).…”

Section: Correlation Of Conformational Mobility With Cytochrome C Actmentioning

confidence: 99%

Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity

Fellner

Parakra

McDonald

et al. 2020

Preprint

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AbstractMutation of cytochrome c in humans causes mild autosomal dominant thrombocytopenia. The role of cytochrome c in platelet formation, and molecular mechanism underlying the association of cytochrome c mutations with thrombocytopenia remains unknown, although a gain-of-function is most likely. Cytochrome c contributes to several cellular processes, with exchange between conformational states proposed to regulate changes in function. Here we use experimental and computational approaches to determine whether pathogenic variants share changes in structure and function, and to understand how these changes might occur. We find that three pathogenic variants (G41S, Y48H, A51V) cause an increase in apoptosome activation and peroxidase activity. Molecular dynamics simulations of these variants, and two non-naturally occurring variants (G41A, G41T), indicate that increased apoptosome activation correlates with increased overall flexibility of cytochrome c, particularly movement of the Ω loops. This suggests that the binding of cytochrome c to apoptotic protease activating factor-1 (Apaf-1) may involve an “induced fit” mechanism which is enhanced in the more conformationally mobile variants. In contrast, peroxidase activity did not significantly correlate with protein dynamics suggesting that the mechanism by which the variants alter peroxidase activity is not related to the conformation dynamics of the hexacoordinate heme Fe state of cytochrome c analyzed in the simulations. Recent suggestions that conformational mobility of specific regions of cytochrome c underpins changes in reduction potential and the alkaline transition pK were not supported. These data highlight that conformational dynamics of cytochrome c drives some but not all of its properties and activities.

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“…3). Because cytochrome c's translocation from the mitochondria to the cytosolic apoptosome complex helps trigger the apoptotic cascade (Bertini et al, 2006), its reduction could inhibit apoptosis. As described above for CAR, the DDF method allows for cytochrome c's localization.…”

Section: Global Proteomics Of Ratsmentioning

confidence: 99%

Global Liver Proteomics of Rats Exposed for 5 Days to Phenobarbital Identifies Changes Associated with Cancer and with CYP Metabolism

Dail

Shack²,

Chambers

et al. 2008

Toxicological Sciences

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A global proteomics approach was applied to model the hepatic response elicited by the toxicologically well-characterized xenobiotic phenobarbital (PB), a prototypical inducer of hepatic xenobiotic metabolizing enzymes and a well-known nongenotoxic liver carcinogen in rats. Differential detergent fractionation two-dimensional liquid chromatography electrospray ionization tandem mass spectrometry and systems biology modeling were used to identify alterations in toxicologically relevant hepatic molecular functions and biological processes in the livers of rats following a 5-day exposure to PB at 80 mg/kg/day or a vehicle control. Of the 3342 proteins identified, expression of 121 (3.6% of the total proteins) was significantly increased and 127 (3.8%) significantly decreased in the PB group compared to controls. The greatest increase was seen for cytochrome P450 (CYP) 2B2 (167-fold). All proteins with statistically significant differences from control were then analyzed using both Gene Ontology (GO) and Ingenuity Pathways Analysis (IPA, 5.0 IPA-Tox) for cellular location, function, network connectivity, and possible disease processes, especially as they relate to CYP-mediated metabolism and nongenotoxic carcinogenesis mechanisms. The GO results suggested that PB's mechanism of nongenotoxic carcinogenesis involves both increased xenobiotic metabolism, especially induction of the 2B subfamily of CYP enzymes, and increased cell cycle activity. Apoptosis, however, also increased, perhaps, as an attempt to counter the rising cancer threat. Of the IPA-mapped proteins, 41 have functions which are procarcinogenic and 14 anticarcinogenic according to the hypothesized nongenotoxic mechanism of imbalance between apoptosis and cellular proliferation. Twenty-two additional IPA nodes can be classified as procarcinogenic by the competing theory of increased metabolism resulting in the formation of reactive oxygen species. Since the systems biology modeling corresponded well to PB effects previously elucidated via more traditional methods, the global proteomic approach is proposed as a new screening methodology that can be incorporated into future toxicological studies.

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Monomorphism of human cytochrome c

Cited by 14 publications

References 13 publications

The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells

The miR-29 transcriptome in endocrine-sensitive and resistant breast cancer cells

Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity

Global Liver Proteomics of Rats Exposed for 5 Days to Phenobarbital Identifies Changes Associated with Cancer and with CYP Metabolism

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