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Article ; Online: An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration.

Tanvir Rahman, M / Kristian Koski, M / Panecka-Hofman, Joanna / Schmitz, Werner / Kastaniotis, Alexander J / Wade, Rebecca C / Wierenga, Rik K / Kalervo Hiltunen, J / Autio, Kaija J

Nature communications

2023 Volume 14, Issue 1, Page(s) 619

Abstract: Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. The structurally well-characterized ... ...

Abstract	Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. The structurally well-characterized component of mtFAS, human 2E-enoyl-ACP reductase (MECR) rescues respiratory growth and lipoylation defects of a Saccharomyces cerevisiae Δetr1 strain lacking native mtFAS enoyl reductase. To address the role of longer products of mtFAS, we employed in silico molecular simulations to design a MECR variant with a shortened substrate binding cavity. Our in vitro and in vivo analyses indicate that the MECR G165Q variant allows synthesis of octanoyl groups but not long chain fatty acids, confirming the validity of our computational approach to engineer substrate length specificity. Furthermore, our data imply that restoring lipoylation in mtFAS deficient yeast strains is not sufficient to support respiration and that long chain acyl-ACPs generated by mtFAS are required for mitochondrial function.
MeSH term(s)	Humans ; Fatty Acids/metabolism ; Mitochondria/genetics ; Mitochondria/metabolism ; Oxidoreductases/metabolism ; Respiration ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)
Chemical Substances	Fatty Acids ; Oxidoreductases (EC 1.-) ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) (EC 1.3.1.9)
Language	English
Publishing date	2023-02-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-36358-7
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Article ; Online: Genetic dissection of the mitochondrial lipoylation pathway in yeast.

Pietikäinen, Laura P / Rahman, M Tanvir / Hiltunen, J Kalervo / Dieckmann, Carol L / Kastaniotis, Alexander J

BMC biology

2021 Volume 19, Issue 1, Page(s) 14

Abstract: Background: Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this ... ...

Abstract	Background: Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this important post-translational modification pathway. Here we used yeast as a model organism to characterize substrate usage by the highly conserved eukaryotic octanoyl/lipoyl transferases in vivo and queried how amenable the lipoylation system is to supplementation with exogenous substrate. Results: We show that the requirement for mitochondrial fatty acid synthesis to provide substrates for lipoylation of the 2-ketoacid dehydrogenases can be bypassed by supplying the cells with free lipoic acid (LA) or octanoic acid (C8) and a mitochondrially targeted fatty acyl/lipoyl activating enzyme. We also provide evidence that the S. cerevisiae lipoyl transferase Lip3, in addition to transferring LA from the glycine cleavage system H protein to the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGD) E2 subunits, can transfer this cofactor from the PDH complex to the KGD complex. In support of yeast as a model system for human metabolism, we demonstrate that the human octanoyl/lipoyl transferases can substitute for their counterparts in yeast to support respiratory growth and protein lipoylation. Like the wild-type yeast enzyme, the human lipoyl transferase LIPT1 responds to LA supplementation in the presence of the activating enzyme LplA. Conclusions: In the yeast model system, the eukaryotic lipoylation pathway can use free LA and C8 as substrates when fatty/lipoic acid activating enzymes are targeted to mitochondria. Lip3 LA transferase has a wider substrate specificity than previously recognized. We show that these features of the lipoylation mechanism in yeast are conserved in mammalian mitochondria. Our findings have important implications for the development of effective therapies for the treatment of LA or mtFAS deficiency-related disorders.
MeSH term(s)	Lipoylation ; Mitochondria/metabolism ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2021-01-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1741-7007
ISSN (online)	1741-7007
DOI	10.1186/s12915-021-00951-3
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Article ; Online: An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration

M. Tanvir Rahman / M. Kristian Koski / Joanna Panecka-Hofman / Werner Schmitz / Alexander J. Kastaniotis / Rebecca C. Wade / Rik K. Wierenga / J. Kalervo Hiltunen / Kaija J. Autio

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 15

Abstract: Mitochondrial fatty acid synthesis (mtFAS) generates the precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. Here, the authors generated an engineered variant of human 2E-enoyl-ACP reductase (MECR) of ... ...

Abstract	Mitochondrial fatty acid synthesis (mtFAS) generates the precursor for lipoic acid synthesis, but the role of longer fatty acid products has remained unclear. Here, the authors generated an engineered variant of human 2E-enoyl-ACP reductase (MECR) of mtFAS to study the role of long chain fatty acids.
Keywords	Science ; Q
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance.

Shvetsova, Antonina / Masud, Ali J / Schneider, Laura / Bergmann, Ulrich / Monteuuis, Geoffray / Miinalainen, Ilkka J / Hiltunen, J Kalervo / Kastaniotis, Alexander J

MicrobiologyOpen

2021 Volume 10, Issue 5, Page(s) e1238

Abstract: Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence ... ...

Abstract	Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence similarities that would allow inferring its functional role are not available. In this work, we describe synthetic petite mutants of GEM1 and UGO1 that depend on the presence of OM45 for respiratory growth, as well as the identification of several multicopy suppressors of the synthetic petite phenotypes. In the analysis of our mutants, we demonstrate that Om45p and Gem1p have a collaborative role in the maintenance of mitochondrial morphology, cristae structure, and mitochondrial DNA maintenance. A group of multicopy suppressors rescuing the synthetic lethal phenotypes of the mutants on non-fermentable carbon sources additionally supports this result. Our results imply that the synthetic petite phenotypes we observed are due to the disturbance of the inner mitochondrial membrane and point to this mitochondrial sub-compartment as the main target of action of Om45p, Ugo1p, and the yeast Miro GTPase Gem1p.
MeSH term(s)	DNA, Fungal ; DNA, Mitochondrial/metabolism ; GTP Phosphohydrolases/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins/genetics ; Mitochondrial Precursor Protein Import Complex Proteins/metabolism ; Mitochondrial Proteins/metabolism ; Mutation ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
Chemical Substances	DNA, Fungal ; DNA, Mitochondrial ; GEM1 protein, S cerevisiae ; Membrane Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins ; Om45 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; UGO1 protein, S cerevisiae ; GTP Phosphohydrolases (EC 3.6.1.-)
Language	English
Publishing date	2021-09-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661368-2
ISSN	2045-8827 ; 2045-8827
ISSN (online)	2045-8827
ISSN	2045-8827
DOI	10.1002/mbo3.1238
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Article ; Online: Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae.

Alam, Jahangir / Rahman, Farah Tazkera / Sah-Teli, Shiv K / Venkatesan, Rajaram / Koski, M Kristian / Autio, Kaija J / Hiltunen, J Kalervo / Kastaniotis, Alexander J

Acta crystallographica. Section D, Structural biology

2021 Volume 77, Issue Pt 6, Page(s) 840–853

Abstract: The Saccharomyces cerevisiae Rsm22 protein (Sc-Rsm22), encoded by the nuclear RSM22 (systematic name YKL155c) gene, is a distant homologue of Rsm22 from Trypanosoma brucei (Tb-Rsm22) and METTL17 from mouse (Mm-METTL17). All three proteins have been shown ...

Abstract	The Saccharomyces cerevisiae Rsm22 protein (Sc-Rsm22), encoded by the nuclear RSM22 (systematic name YKL155c) gene, is a distant homologue of Rsm22 from Trypanosoma brucei (Tb-Rsm22) and METTL17 from mouse (Mm-METTL17). All three proteins have been shown to be associated with mitochondrial gene expression, and Sc-Rsm22 has been documented to be essential for mitochondrial respiration. The Sc-Rsm22 protein comprises a polypeptide of molecular weight 72.2 kDa that is predicted to harbor an N-terminal mitochondrial targeting sequence. The precise physiological function of Rsm22-family proteins is unknown, and no structural information has been available for Sc-Rsm22 to date. In this study, Sc-Rsm22 was expressed and purified in monomeric and dimeric forms, their folding was confirmed by circular-dichroism analyses and their low-resolution structures were determined using a small-angle X-ray scattering (SAXS) approach. The solution structure of the monomeric form of Sc-Rsm22 revealed an elongated three-domain arrangement, which differs from the shape of Tb-Rsm22 in its complex with the mitochondrial small ribosomal subunit in T. brucei (PDB entry 6sg9). A bioinformatic analysis revealed that the core domain in the middle (Leu117-Asp462 in Sc-Rsm22) resembles the corresponding region in Tb-Rsm22, including a Rossmann-like methyltransferase fold followed by a zinc-finger-like structure. The latter structure is not present in this position in other methyltransferases and is therefore a unique structural motif for this family. The first half of the C-terminal domain is likely to form an OB-fold, which is typically found in RNA-binding proteins and is also seen in the Tb-Rsm22 structure. In contrast, the N-terminal domain of Sc-Rsm22 is predicted to be fully α-helical and shares no sequence similarity with other family members. Functional studies demonstrated that the monomeric variant of Sc-Rsm22 methylates mitochondrial tRNAs in vitro. These data suggest that Sc-Rsm22 is a new and unique member of the RNA methyltransferases that is important for mitochondrial protein synthesis.
MeSH term(s)	Models, Molecular ; Protein Structural Elements ; Ribosomal Proteins/chemistry ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/chemistry
Chemical Substances	Ribosomal Proteins ; Rsm22 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2021-05-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798321004149
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Article ; Online: Different opinion on the reported role of Poldip2 and ACSM1 in a mammalian lipoic acid salvage pathway controlling HIF-1 activation.

Bailey, Peter S J / Hiltunen, J Kalervo / Dieckmann, Carol L / Kastaniotis, Alexander J / Nathan, James A

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 32, Page(s) E7458–E7459

MeSH term(s)	Animals ; Attitude ; Hypoxia-Inducible Factor 1 ; Thioctic Acid
Chemical Substances	Hypoxia-Inducible Factor 1 ; Thioctic Acid (73Y7P0K73Y)
Language	English
Publishing date	2018-07-24
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1804041115
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Article ; Online: Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites.

Sridhar, Shruthi / Schmitz, Werner / Hiltunen, J Kalervo / Venkatesan, Rajaram / Bergmann, Ulrich / Kiema, Tiila Riikka / Wierenga, Rikkert K

Acta crystallographica. Section D, Structural biology

2020 Volume 76, Issue Pt 12, Page(s) 1256–1269

Abstract: The peroxisomal multifunctional enzyme type 1 (MFE1) catalyzes two successive reactions in the β-oxidation cycle: the 2E-enoyl-CoA hydratase (ECH) and ... ...

Abstract	The peroxisomal multifunctional enzyme type 1 (MFE1) catalyzes two successive reactions in the β-oxidation cycle: the 2E-enoyl-CoA hydratase (ECH) and NAD
MeSH term(s)	Animals ; Binding Sites ; Enoyl-CoA Hydratase/chemistry ; Enoyl-CoA Hydratase/metabolism ; Models, Molecular ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Protein Binding ; Rats
Chemical Substances	Ehhadh protein, rat ; Multienzyme Complexes ; Enoyl-CoA Hydratase (EC 4.2.1.17)
Language	English
Publishing date	2020-11-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2968623-4
ISSN	2059-7983 ; 0907-4449
ISSN (online)	2059-7983
ISSN	0907-4449
DOI	10.1107/S2059798320013819
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Article ; Online: Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function.

Masud, Ali J / Kastaniotis, Alexander J / Rahman, M Tanvir / Autio, Kaija J / Hiltunen, J Kalervo

Biochimica et biophysica acta. Molecular cell research

2019 Volume 1866, Issue 12, Page(s) 118540

Abstract: Acyl carrier protein (ACP) is a principal partner in the cytosolic and mitochondrial fatty acid synthesis (FAS) pathways. The active form holo-ACP serves as FAS platform, using its 4'-phosphopantetheine group to present covalently attached FAS ... ...

Abstract	Acyl carrier protein (ACP) is a principal partner in the cytosolic and mitochondrial fatty acid synthesis (FAS) pathways. The active form holo-ACP serves as FAS platform, using its 4'-phosphopantetheine group to present covalently attached FAS intermediates to the enzymes responsible for the acyl chain elongation process. Mitochondrial unacylated holo-ACP is a component of mammalian mitoribosomes, and acylated ACP species participate as interaction partners in several ACP-LYRM (leucine-tyrosine-arginine motif)-protein heterodimers that act either as assembly factors or subunits of the electron transport chain and Fe-S cluster assembly complexes. Moreover, octanoyl-ACP provides the C8 backbone for endogenous lipoic acid synthesis. Accumulating evidence suggests that mtFAS-generated acyl-ACPs act as signaling molecules in an intramitochondrial metabolic state sensing circuit, coordinating mitochondrial acetyl-CoA levels with mitochondrial respiration, Fe-S cluster biogenesis and protein lipoylation.
MeSH term(s)	Acetyl Coenzyme A/metabolism ; Acyl Carrier Protein/genetics ; Acyl Carrier Protein/metabolism ; Amino Acid Sequence ; Animals ; Humans ; Mitochondria/metabolism ; Sequence Alignment
Chemical Substances	Acyl Carrier Protein ; Acetyl Coenzyme A (72-89-9)
Language	English
Publishing date	2019-08-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	60-7
ISSN	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamcr.2019.118540
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Article ; Online: Genetic dissection of the mitochondrial lipoylation pathway in yeast

Laura P. Pietikäinen / M. Tanvir Rahman / J. Kalervo Hiltunen / Carol L. Dieckmann / Alexander J. Kastaniotis

BMC Biology, Vol 19, Iss 1, Pp 1-

2021 Volume 15

Abstract: Abstract Background Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of ... ...

Abstract	Abstract Background Lipoylation of 2-ketoacid dehydrogenases is essential for mitochondrial function in eukaryotes. While the basic principles of the lipoylation processes have been worked out, we still lack a thorough understanding of the details of this important post-translational modification pathway. Here we used yeast as a model organism to characterize substrate usage by the highly conserved eukaryotic octanoyl/lipoyl transferases in vivo and queried how amenable the lipoylation system is to supplementation with exogenous substrate. Results We show that the requirement for mitochondrial fatty acid synthesis to provide substrates for lipoylation of the 2-ketoacid dehydrogenases can be bypassed by supplying the cells with free lipoic acid (LA) or octanoic acid (C8) and a mitochondrially targeted fatty acyl/lipoyl activating enzyme. We also provide evidence that the S. cerevisiae lipoyl transferase Lip3, in addition to transferring LA from the glycine cleavage system H protein to the pyruvate dehydrogenase (PDH) and α-ketoglutarate dehydrogenase (KGD) E2 subunits, can transfer this cofactor from the PDH complex to the KGD complex. In support of yeast as a model system for human metabolism, we demonstrate that the human octanoyl/lipoyl transferases can substitute for their counterparts in yeast to support respiratory growth and protein lipoylation. Like the wild-type yeast enzyme, the human lipoyl transferase LIPT1 responds to LA supplementation in the presence of the activating enzyme LplA. Conclusions In the yeast model system, the eukaryotic lipoylation pathway can use free LA and C8 as substrates when fatty/lipoic acid activating enzymes are targeted to mitochondria. Lip3 LA transferase has a wider substrate specificity than previously recognized. We show that these features of the lipoylation mechanism in yeast are conserved in mammalian mitochondria. Our findings have important implications for the development of effective therapies for the treatment of LA or mtFAS deficiency-related disorders.
Keywords	Lipoylation ; Mitochondrial fatty acid synthesis (mtFAS) ; Octanoyl/lipoyl transferases ; S. cerevisiae model ; Supplementation studies ; Lip3/LIPT1 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: 17B-hydroxysteroid dehydrogenases as acyl thioester metabolizing enzymes.

Hiltunen, J Kalervo / Kastaniotis, Alexander J / Autio, Kaija J / Jiang, Guangyu / Chen, Zhijun / Glumoff, Tuomo

Molecular and cellular endocrinology

2018 Volume 489, Page(s) 107–118

Abstract: 17β-Hydroxysteroid dehydrogenases (HSD17B) catalyze the oxidation/reduction of 17β-hydroxy/keto group in position C17 in C18- and C19 steroids. Most HSD17Bs are also catalytically active with substrates other than steroids. A subset of these enzymes is ... ...

Abstract	17β-Hydroxysteroid dehydrogenases (HSD17B) catalyze the oxidation/reduction of 17β-hydroxy/keto group in position C17 in C18- and C19 steroids. Most HSD17Bs are also catalytically active with substrates other than steroids. A subset of these enzymes is able to process thioesters of carboxylic acids. This group of enzymes includes HSD17B4, HSD17B8, HSD17B10 and HSD17B12, which execute reactions in intermediary metabolism, participating in peroxisomal β-oxidation of fatty acids, mitochondrial oxidation of 3R-hydroxyacyl-groups, breakdown of isoleucine and fatty acid chain elongation in endoplasmic reticulum. Divergent substrate acceptance capabilities exemplify acquirement of catalytic site adaptiveness during evolution. As an additional common feature these HSD17Bs are multifunctional enzymes that arose either via gene fusions (HSD17B4) or are incorporated as subunits into multifunctional protein complexes (HSD17B8 and HSD17B10). Crystal structures of HSD17B4, HSD17B8 and HSD17B10 give insight into their structure-function relationships. Thus far, deficiencies of HSD17B4 and HSD17B10 have been assigned to inborn errors in humans, underlining their significance as enzymes of metabolism.
MeSH term(s)	17-Hydroxysteroid Dehydrogenases/chemistry ; 17-Hydroxysteroid Dehydrogenases/metabolism ; Animals ; Disease ; Esters/metabolism ; Fatty Acids, Unsaturated/metabolism ; Humans ; Mitochondria/metabolism ; RNA/metabolism
Chemical Substances	Esters ; Fatty Acids, Unsaturated ; RNA (63231-63-0) ; 17-Hydroxysteroid Dehydrogenases (EC 1.1.-) ; 3 (or 17)-beta-hydroxysteroid dehydrogenase (EC 1.1.1.51)
Language	English
Publishing date	2018-11-30
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	187438-x
ISSN	1872-8057 ; 0303-7207
ISSN (online)	1872-8057
ISSN	0303-7207
DOI	10.1016/j.mce.2018.11.012
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