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Article ; Online: Stimulation of Variant Forms of the Mitochondrial DNA Helicase Twinkle by the Mitochondrial Single-Stranded DNA-Binding Protein.

Rodrigues, Ana P C / Oliveira, Marcos T

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2281, Page(s) 313–322

Abstract: Defects in mitochondrial DNA (mtDNA) maintenance may lead to disturbances in mitochondrial homeostasis and energy production in eukaryotic cells, causing diseases. During mtDNA replication, the mitochondrial single-stranded DNA-binding protein (mtSSB) ... ...

Abstract	Defects in mitochondrial DNA (mtDNA) maintenance may lead to disturbances in mitochondrial homeostasis and energy production in eukaryotic cells, causing diseases. During mtDNA replication, the mitochondrial single-stranded DNA-binding protein (mtSSB) stabilizes and protects the exposed single-stranded mtDNA from nucleolysis; perhaps more importantly, it appears to coordinate the actions of both the replicative mtDNA helicase Twinkle and DNA polymerase gamma at the replication fork. Here, we describe a helicase stimulation protocol to test in vitro the functional interaction between mtSSB and variant forms of Twinkle. We show for the first time that the C-terminal tail of Twinkle is important for such an interaction, and that it negatively regulates helicase unwinding activity in a salt-dependent manner.
MeSH term(s)	Binding Sites ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Replication ; DNA, Mitochondrial/chemistry ; DNA, Mitochondrial/metabolism ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Humans ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation
Chemical Substances	DNA, Mitochondrial ; DNA, Single-Stranded ; DNA-Binding Proteins ; Mitochondrial Proteins ; SSBP1 protein, human ; DNA Helicases (EC 3.6.4.-) ; TWNK protein, human (EC 3.6.4.12)
Language	English
Publishing date	2021-04-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1290-3_20
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Article ; Online: Mitochondrial DNA maintenance in Drosophila melanogaster.

Rodrigues, Ana P C / Novaes, Audrey C / Ciesielski, Grzegorz L / Oliveira, Marcos T

Bioscience reports

2022 Volume 42, Issue 11

Abstract: All 37 mitochondrial DNA (mtDNA)-encoded genes involved with oxidative phosphorylation and intramitochondrial protein synthesis, and several nuclear-encoded genes involved with mtDNA replication, transcription, repair and recombination are conserved ... ...

Abstract	All 37 mitochondrial DNA (mtDNA)-encoded genes involved with oxidative phosphorylation and intramitochondrial protein synthesis, and several nuclear-encoded genes involved with mtDNA replication, transcription, repair and recombination are conserved between the fruit fly Drosophila melanogaster and mammals. This, in addition to its easy genetic tractability, has made Drosophila a useful model for our understanding of animal mtDNA maintenance and human mtDNA diseases. However, there are key differences between the Drosophila and mammalian systems that feature the diversity of mtDNA maintenance processes inside animal cells. Here, we review what is known about mtDNA maintenance in Drosophila, highlighting areas for which more research is warranted and providing a perspective preliminary in silico and in vivo analyses of the tissue specificity of mtDNA maintenance processes in this model organism. Our results suggest new roles (or the lack thereof) for well-known maintenance proteins, such as the helicase Twinkle and the accessory subunit of DNA polymerase γ, and for other Drosophila gene products that may even aid in shedding light on mtDNA maintenance in other animals. We hope to provide the reader some interesting paths that can be taken to help our community show how Drosophila may impact future mtDNA maintenance research.
MeSH term(s)	Animals ; Humans ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Mitochondria/genetics ; Mitochondria/metabolism ; DNA Polymerase gamma/genetics ; DNA Polymerase gamma/metabolism ; Drosophila Proteins/metabolism ; DNA Replication/genetics ; Mitochondrial Proteins/genetics ; Mammals/metabolism
Chemical Substances	DNA, Mitochondrial ; DNA Polymerase gamma (EC 2.7.7.7) ; Drosophila Proteins ; Mitochondrial Proteins
Language	English
Publishing date	2022-12-02
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20211693
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Article ; Online: Xenotopic expression of alternative electron transport enzymes in animal mitochondria and their impact in health and disease.

Camargo, André F / Chioda, Marina M / Rodrigues, Ana P C / Garcia, Geovana S / McKinney, Emily A / Jacobs, Howard T / Oliveira, Marcos T

Cell biology international

2018 Volume 42, Issue 6, Page(s) 664–669

Abstract: The mitochondrial respiratory chain in vertebrates and arthropods is different from that of most other eukaryotes because they lack alternative enzymes that provide electron transfer pathways additional to the oxidative phosphorylation (OXPHOS) system. ... ...

Abstract	The mitochondrial respiratory chain in vertebrates and arthropods is different from that of most other eukaryotes because they lack alternative enzymes that provide electron transfer pathways additional to the oxidative phosphorylation (OXPHOS) system. However, the use of diverse experimental models, such as human cells in culture, Drosophila melanogaster and the mouse, has demonstrated that the transgenic expression of these alternative enzymes can impact positively many phenotypes associated with human mitochondrial and other cellular dysfunction, including those typically presented in complex IV deficiencies, Parkinson's, and Alzheimer's. In addition, these enzymes have recently provided extremely valuable data on how, when, and where reactive oxygen species, considered by many as "by-products" of OXPHOS, can contribute to animal longevity. It has also been shown that the expression of the alternative enzymes is thermogenic in cultured cells, causes reproductive defects in flies, and enhances the deleterious phenotype of some mitochondrial disease models. Therefore, all the reported beneficial effects must be considered with caution, as these enzymes have been proposed to be deployed in putative gene therapies to treat human diseases. Here, we present a brief review of the scientific data accumulated over the past decade that show the benefits and the risks of introducing alternative branches of the electron transport into mammalian and insect mitochondria, and we provide a perspective on the future of this research field.
MeSH term(s)	Adenine Nucleotide Translocator 1/genetics ; Adenine Nucleotide Translocator 1/metabolism ; Animals ; Animals, Genetically Modified/growth & development ; Animals, Genetically Modified/metabolism ; Electron Transport Chain Complex Proteins/genetics ; Electron Transport Chain Complex Proteins/metabolism ; Humans ; Mitochondria/metabolism ; NADH Dehydrogenase/genetics ; NADH Dehydrogenase/metabolism ; Oxidative Phosphorylation ; Reactive Oxygen Species/metabolism
Chemical Substances	Adenine Nucleotide Translocator 1 ; Electron Transport Chain Complex Proteins ; Reactive Oxygen Species ; NADH Dehydrogenase (EC 1.6.99.3)
Language	English
Publishing date	2018-02-23
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1143453-3
ISSN	1095-8355 ; 1065-6995
ISSN (online)	1095-8355
ISSN	1065-6995
DOI	10.1002/cbin.10943
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Article ; Online: sgTarget: a target selection resource for structural genomics.

Rodrigues, Ana P C / Grant, Barry J / Hubbard, Roderick E

Nucleic acids research

2006 Volume 34, Issue Web Server issue, Page(s) W225–30

Abstract: sgTarget (http://www.ysbl.york.ac.uk/sgTarget) is a web-based resource to aid the selection and prioritization of candidate proteins for structure determination. The system annotates user submitted gene or protein sequences, identifying sequence families ...

Abstract	sgTarget (http://www.ysbl.york.ac.uk/sgTarget) is a web-based resource to aid the selection and prioritization of candidate proteins for structure determination. The system annotates user submitted gene or protein sequences, identifying sequence families with no homologues of known structure, and characterizing each protein according to a range of physicochemical properties that may affect its expression, solubility and likelihood to crystallize. Summaries of these analyses are available for individual sequences, as well as whole datasets. This type of analysis enables structural biologists to iteratively select targets from their genomic sequences of interest and according to their research needs. All sequence datasets submitted to sgTarget are available for users to select and rank using their choice of criteria. sgTarget was developed to support individual laboratories collaborating in structural and functional genomics projects and should be valuable to structural biologists wishing to employ the wealth of available genome sequences in their structural quests.
MeSH term(s)	Animals ; Genomics ; Internet ; Plasmodium falciparum/genetics ; Protein Conformation ; Proteins/chemistry ; Proteins/genetics ; Protozoan Proteins/chemistry ; Sequence Analysis, Protein ; Software ; User-Computer Interface
Chemical Substances	Proteins ; Protozoan Proteins
Language	English
Publishing date	2006-07-01
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205588-5
ISSN	1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
ISSN (online)	1362-4962 ; 1746-8272
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nar/gkl121
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Article ; Online: The 2006 automated function prediction meeting.

Rodrigues, Ana P C / Grant, Barry J / Godzik, Adam / Friedberg, Iddo

BMC bioinformatics

2007 Volume 8 Suppl 4, Page(s) S1–4

MeSH term(s)	Computational Biology ; Proteins/chemistry
Chemical Substances	Proteins
Language	English
Publishing date	2007-05-22
Publishing country	England
Document type	Congress
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/1471-2105-8-S4-S1
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Article ; Online: RPN-6 determines C. elegans longevity under proteotoxic stress conditions.

Vilchez, David / Morantte, Ianessa / Liu, Zheng / Douglas, Peter M / Merkwirth, Carsten / Rodrigues, Ana P C / Manning, Gerard / Dillin, Andrew

Nature

2012 Volume 489, Issue 7415, Page(s) 263–268

Abstract: Organisms that protect their germ-cell lineages from damage often do so at considerable cost: limited metabolic resources become partitioned away from maintenance of the soma, leaving the ageing somatic tissues to navigate survival amid an environment ... ...

Abstract	Organisms that protect their germ-cell lineages from damage often do so at considerable cost: limited metabolic resources become partitioned away from maintenance of the soma, leaving the ageing somatic tissues to navigate survival amid an environment containing damaged and poorly functioning proteins. Historically, experimental paradigms that limit reproductive investment result in lifespan extension. We proposed that germline-deficient animals might exhibit heightened protection from proteotoxic stressors in somatic tissues. We find that the forced re-investment of resources from the germ line to the soma in Caenorhabditis elegans results in elevated somatic proteasome activity, clearance of damaged proteins and increased longevity. This activity is associated with increased expression of rpn-6, a subunit of the 19S proteasome, by the FOXO transcription factor DAF-16. Ectopic expression of rpn-6 is sufficient to confer proteotoxic stress resistance and extend lifespan, indicating that rpn-6 is a candidate to correct deficiencies in age-related protein homeostasis disorders.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans/physiology ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Cell Separation ; Female ; Forkhead Transcription Factors ; Gene Expression Regulation ; Germ Cells/cytology ; Germ Cells/metabolism ; Heat-Shock Response/genetics ; Homeostasis/radiation effects ; Longevity/genetics ; Longevity/physiology ; Longevity/radiation effects ; Male ; Mutation/genetics ; Oxidative Stress/physiology ; Peptides/metabolism ; Proteasome Endopeptidase Complex/chemistry ; Proteasome Endopeptidase Complex/genetics ; Proteasome Endopeptidase Complex/metabolism ; Stress, Physiological/physiology ; Stress, Physiological/radiation effects ; Transcription Factors/metabolism ; Ultraviolet Rays
Chemical Substances	Caenorhabditis elegans Proteins ; Forkhead Transcription Factors ; Peptides ; Transcription Factors ; daf-16 protein, C elegans ; polyglutamine (26700-71-0) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; RPN-6.1 protein, C elegans (EC 3.4.25.1)
Language	English
Publishing date	2012-08-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature11315
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Article: sgTarget: a target selection resource for structural genomics

Rodrigues, Ana P.C / Grant, Barry J / Hubbard, Roderick E

Nucleic acids research. 2006 July 1, v. 34, no. suppl_2

2006

Abstract	sgTarget (http://www.ysbl.york.ac.uk/sgTarget) is a web-based resource to aid the selection and prioritization of candidate proteins for structure determination. The system annotates user submitted gene or protein sequences, identifying sequence families with no homologues of known structure, and characterizing each protein according to a range of physicochemical properties that may affect its expression, solubility and likelihood to crystallize. Summaries of these analyses are available for individual sequences, as well as whole datasets. This type of analysis enables structural biologists to iteratively select targets from their genomic sequences of interest and according to their research needs. All sequence datasets submitted to sgTarget are available for users to select and rank using their choice of criteria. sgTarget was developed to support individual laboratories collaborating in structural and functional genomics projects and should be valuable to structural biologists wishing to employ the wealth of available genome sequences in their structural quests.
Keywords	Internet ; amino acid sequences ; data collection ; genes ; genomics ; nucleic acids ; nucleotide sequences ; prioritization ; proteins ; solubility
Language	English
Dates of publication	2006-0701
Size	p. W225-W230.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB.

Mair, William / Morantte, Ianessa / Rodrigues, Ana P C / Manning, Gerard / Montminy, Marc / Shaw, Reuben J / Dillin, Andrew

Nature

2011 Volume 470, Issue 7334, Page(s) 404–408

Abstract: Activating AMPK or inactivating calcineurin slows ageing in Caenorhabditis elegans and both have been implicated as therapeutic targets for age-related pathology in mammals. However, the direct targets that mediate their effects on longevity remain ... ...

Abstract	Activating AMPK or inactivating calcineurin slows ageing in Caenorhabditis elegans and both have been implicated as therapeutic targets for age-related pathology in mammals. However, the direct targets that mediate their effects on longevity remain unclear. In mammals, CREB-regulated transcriptional coactivators (CRTCs) are a family of cofactors involved in diverse physiological processes including energy homeostasis, cancer and endoplasmic reticulum stress. Here we show that both AMPK and calcineurin modulate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC. We demonstrate that CRTC-1 is a direct AMPK target, and interacts with the CREB homologue-1 (CRH-1) transcription factor in vivo. The pro-longevity effects of activating AMPK or deactivating calcineurin decrease CRTC-1 and CRH-1 activity and induce transcriptional responses similar to those of CRH-1 null worms. Downregulation of crtc-1 increases lifespan in a crh-1-dependent manner and directly reducing crh-1 expression increases longevity, substantiating a role for CRTCs and CREB in ageing. Together, these findings indicate a novel role for CRTCs and CREB in determining lifespan downstream of AMPK and calcineurin, and illustrate the molecular mechanisms by which an evolutionarily conserved pathway responds to low energy to increase longevity.
MeSH term(s)	AMP-Activated Protein Kinases/metabolism ; Aging/metabolism ; Aging/physiology ; Animals ; Caenorhabditis elegans/enzymology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans/physiology ; Caenorhabditis elegans Proteins/biosynthesis ; Caenorhabditis elegans Proteins/chemistry ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Calcineurin/metabolism ; Calcineurin Inhibitors ; Cyclic AMP Response Element-Binding Protein/biosynthesis ; Cyclic AMP Response Element-Binding Protein/metabolism ; Down-Regulation ; Energy Metabolism ; Enzyme Activation ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Longevity/genetics ; Longevity/physiology ; Phosphorylation ; Protein-Serine-Threonine Kinases/metabolism ; Trans-Activators/chemistry ; Trans-Activators/deficiency ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Transcription Factors/biosynthesis ; Transcription Factors/metabolism ; Transcription, Genetic
Chemical Substances	CRH-1 protein, C elegans ; CRTC-1 protein, C elegans ; Caenorhabditis elegans Proteins ; Calcineurin Inhibitors ; Cyclic AMP Response Element-Binding Protein ; Trans-Activators ; Transcription Factors ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; AAK-2 protein, C elegans (EC 2.7.11.31) ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; Calcineurin (EC 3.1.3.16)
Language	English
Publishing date	2011-02-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature09706
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Article: The challenge of protein structure determination--lessons from structural genomics.

Slabinski, Lukasz / Jaroszewski, Lukasz / Rodrigues, Ana P C / Rychlewski, Leszek / Wilson, Ian A / Lesley, Scott A / Godzik, Adam

Protein science : a publication of the Protein Society

2007 Volume 16, Issue 11, Page(s) 2472–2482

Abstract: The process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high-throughput structure determination in structural genomics centers, we can now ... ...

Abstract	The process of experimental determination of protein structure is marred with a high ratio of failures at many stages. With availability of large quantities of data from high-throughput structure determination in structural genomics centers, we can now learn to recognize protein features correlated with failures; thus, we can recognize proteins more likely to succeed and eventually learn how to modify those that are less likely to succeed. Here, we identify several protein features that correlate strongly with successful protein production and crystallization and combine them into a single score that assesses "crystallization feasibility." The formula derived here was tested with a jackknife procedure and validated on independent benchmark sets. The "crystallization feasibility" score described here is being applied to target selection in the Joint Center for Structural Genomics, and is now contributing to increasing the success rate, lowering the costs, and shortening the time for protein structure determination. Analyses of PDB depositions suggest that very similar features also play a role in non-high-throughput structure determination, suggesting that this crystallization feasibility score would also be of significant interest to structural biology, as well as to molecular and biochemistry laboratories.
MeSH term(s)	Computational Biology/methods ; Crystallization ; Crystallography, X-Ray/methods ; Databases, Protein ; Genomics/methods ; Isoelectric Focusing ; Magnetic Resonance Spectroscopy/methods ; Probability ; Protein Conformation ; Protein Structure, Secondary ; Proteins/chemistry ; Proteomics/methods ; Sequence Analysis, Protein
Chemical Substances	Proteins
Language	English
Publishing date	2007-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1110/ps.073037907
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Article ; Online: Bio3d: an R package for the comparative analysis of protein structures.

Grant, Barry J / Rodrigues, Ana P C / ElSawy, Karim M / McCammon, J Andrew / Caves, Leo S D

Bioinformatics (Oxford, England)

2006 Volume 22, Issue 21, Page(s) 2695–2696

Abstract: Unlabelled: An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for ... ...

Abstract	Unlabelled: An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data. Availability: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/
MeSH term(s)	Amino Acid Sequence ; Computer Simulation ; Internet ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Proteins/chemistry ; Sequence Analysis, Protein/methods ; Software ; User-Computer Interface
Chemical Substances	Proteins
Language	English
Publishing date	2006-11-01
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btl461
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