MAPR origins reveal a new class of prokaryotic cytochrome b5 proteins and possible role in eukaryogenesis

The multiple functions of PGRMC1, the archetypal heme-binding eukaryotic MAPR family member, include steroidogenic regulation, membrane trafficking, and steroid responsiveness. The interrelationships between these functions are currently poorly understood. Previous work has shown that different MAPR subclasses were present early in eukaryotic evolution, and that tyrosine phosphorylated residues appeared in the eumetazoan ancestor, coincident with a gastrulation organizer. Here we show that MAPR proteins are related to a newly recognized class of prokaryotic cytochrome-b5 domain proteins. Our first solved structure of this new class exhibits shared MAPR-like folded architecture and heme-binding orientation. We also report that a protein subgroup from Candidate Phyla Radiation (CPR) bacteria shares MAPR-like heme-interacting tyrosines. Our results support bacterial origins for both PGRMC1 and CYP51A, that catalyze the meiosis-associated 14-demethylation of the first sterol lanosterol from yeast to humans. We propose that eukaryotic acquisition of a membrane-trafficking function related to sterol metabolism was associated with the appearance of MAPR genes early in eukaryotic evolution.

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Structural characterization of a MAPR-related archaeal cytochrome b5M protein

10.1101/2021.11.30.470528 ◽

2021 ◽

Author(s):

Sarah Teakel ◽

Michealla Marama ◽

David Aragão ◽

Sofiya Tsimbalyuk ◽

Jade K. Forwood ◽

...

Keyword(s):

Crystal Structure ◽

Progesterone Receptor ◽

Structural Characterization ◽

Cytochrome B5 ◽

Unique Sequence ◽

Heme Binding ◽

Accession Number ◽

New Class ◽

Sequence Elements

We recently reported that the membrane associated progesterone receptor (MAPR) protein family (mammalian members: PGRMC1, PGRMC2, NEUFC and NENF) originated from a new class of prokaryotic cytochrome b5 (cytb5) domain proteins, called cytb5M (MAPR-like). Relative to classical cytb5 proteins, MAPR and ctyb5M proteins shared unique sequence elements and a distinct heme binding orientation at an approximately 90⁰ rotation relative to classical cytb5, as demonstrated in the archetypal crystal structure of a cytb5M protein (PDB accession number 6NZX). Here, we present the second crystal structure of an archaeal cytb5M domain (Methanococcoides burtonii WP_011499504.1, PDB:6VZ6). It exhibits similar heme-binding to the 6NZX cytb5M, supporting the deduction that MAPR-like heme orientation was inherited from the prokaryotic ancestor of the original eukaryotic MAPR gene.

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The Effect of Heme Binding on the Tryptophan Residue and the Protein Conformation of Cytochrome b5

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)45035-7 ◽

1972 ◽

Vol 247 (14) ◽

pp. 4641-4647 ◽

Cited By ~ 1

Author(s):

Thomas E. Huntley ◽

Philipp Strittmatter

Keyword(s):

Protein Conformation ◽

Cytochrome B5 ◽

Tryptophan Residue ◽

Heme Binding

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The Nature of the Heme Binding in Microsomal Cytochrome b5

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)64647-2 ◽

1960 ◽

Vol 235 (8) ◽

pp. 2492-2497 ◽

Cited By ~ 20

Author(s):

Philipp Strittmatter

Keyword(s):

Cytochrome B5 ◽

Heme Binding ◽

Microsomal Cytochrome ◽

Microsomal Cytochrome B5

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A New Class of Repression Modules Is Critical for Heme Regulation of the Yeast Transcriptional Activator Hap1

Molecular and Cellular Biology ◽

10.1128/mcb.19.6.4324 ◽

1999 ◽

Vol 19 (6) ◽

pp. 4324-4333 ◽

Cited By ~ 30

Author(s):

Angela Hach ◽

Thomas Hon ◽

Li Zhang

Keyword(s):

Biochemical Analysis ◽

Activator Protein 1 ◽

Heme Binding ◽

Systematic Analysis ◽

High Molecular Weight Complex ◽

Cellular Processes ◽

New Class ◽

Heme Domain ◽

Heme Regulation

ABSTRACTHeme plays key regulatory roles in numerous molecular and cellular processes for systems that sense or use oxygen. In the yeastSaccharomyces cerevisiae, oxygen sensing and heme signaling are mediated by heme activator protein 1 (Hap1). Hap1 contains seven heme-responsive motifs (HRMs): six are clustered in the heme domain, and a seventh is near the activation domain. To determine the functional role of HRMs and to define which parts of Hap1 mediate heme regulation, we carried out a systematic analysis of Hap1 mutants with various regions deleted or mutated. Strikingly, the data show that HRM1 to -6, located in the previously designated Hap1 heme domain, have little impact on heme regulation. All seven HRMs are dispensable for Hap1 repression in the absence of heme, but HRM7 is required for Hap1 activation by heme. More importantly, we show that a novel class of repression modules—RPM1, encompassing residues 245 to 278; RPM2, encompassing residues 1061 to 1185; and RPM3, encompassing residues 203 to 244—is critical for Hap1 repression in the absence of heme. Biochemical analysis indicates that RPMs mediate Hap1 repression, at least partly, by the formation of a previously identified higher-order complex termed the high-molecular-weight complex (HMC), while HRMs mediate heme activation by permitting heme binding and the disassembly of the HMC. These findings provide significant new insights into the molecular interactions critical for Hap1 repression in the absence of heme and Hap1 activation by heme.

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Phospholipid membranes affect tertiary structure of the soluble cytochrome b5 heme-binding domain

Biochimica et Biophysica Acta (BBA) - Biomembranes ◽

10.1016/j.bbamem.2007.12.028 ◽

2008 ◽

Vol 1778 (4) ◽

pp. 1015-1026 ◽

Cited By ~ 8

Author(s):

Liana V. Basova ◽

Elisaveta I. Tiktopulo ◽

Victor P. Kutyshenko ◽

A. Grant Mauk ◽

Valentina E. Bychkova

Keyword(s):

Tertiary Structure ◽

Cytochrome B5 ◽

Binding Domain ◽

Phospholipid Membranes ◽

Heme Binding

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The WASP Homologue Las17 Activates the Novel Actin-regulatory Activity of Ysc84 to Promote Endocytosis in Yeast

Molecular Biology of the Cell ◽

10.1091/mbc.e08-09-0982 ◽

2009 ◽

Vol 20 (6) ◽

pp. 1618-1628 ◽

Cited By ~ 24

Author(s):

Alastair S. Robertson ◽

Ellen G. Allwood ◽

Adam P.C. Smith ◽

Fiona C. Gardiner ◽

Rosaria Costa ◽

...

Keyword(s):

Membrane Trafficking ◽

Actin Polymerization ◽

Actin Binding ◽

The Novel ◽

Cellular Processes ◽

New Class ◽

Actin Binding Domain ◽

Kinetics Of ◽

Actin Binding Site

Actin plays an essential role in many eukaryotic cellular processes, including motility, generation of polarity, and membrane trafficking. Actin function in these roles is regulated by association with proteins that affect its polymerization state, dynamics, and organization. Numerous proteins have been shown to localize with cortical patches of yeast actin during endocytosis, but the role of many of these proteins remains poorly understood. Here, we reveal that the yeast protein Ysc84 represents a new class of actin-binding proteins, conserved from yeast to humans. It contains a novel N-terminal actin-binding domain termed Ysc84 actin binding (YAB), which can bind and bundle actin filaments. Intriguingly, full-length Ysc84 alone does not bind to actin, but binding can be activated by a specific motif within the polyproline region of the yeast WASP homologue Las17. We also identify a new monomeric actin-binding site on Las17. Together, the polyproline region of Las17 and Ysc84 can promote actin polymerization. Using live cell imaging, kinetics of assembly and disassembly of proteins at the endocytic site were analyzed and reveal that loss of Ysc84 and its homologue Lsb3 decrease inward movement of vesicles consistent with a role in actin polymerization during endocytosis.

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Characterization of TSET, an ancient and widespread membrane trafficking complex

eLife ◽

10.7554/elife.02866 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 63

Author(s):

Jennifer Hirst ◽

Alexander Schlacht ◽

John P Norcott ◽

David Traynor ◽

Gareth Bloomfield ◽

...

Keyword(s):

Plasma Membrane ◽

Membrane Trafficking ◽

Scaffolding Proteins ◽

Eukaryotic Evolution ◽

Bioinformatics Tool ◽

Membrane Turnover ◽

Evolutionary Path ◽

The Core ◽

Eukaryotic Supergroup

The heterotetrameric AP and F-COPI complexes help to define the cellular map of modern eukaryotes. To search for related machinery, we developed a structure-based bioinformatics tool, and identified the core subunits of TSET, a 'missing link' between the APs and COPI. Studies in Dictyostelium indicate that TSET is a heterohexamer, with two associated scaffolding proteins. TSET is non-essential in Dictyostelium, but may act in plasma membrane turnover, and is essentially identical to the recently described TPLATE complex, TPC. However, whereas TPC was reported to be plant-specific, we can identify a full or partial complex in every eukaryotic supergroup. An evolutionary path can be deduced from the earliest origins of the heterotetramer/scaffold coat to its multiple manifestations in modern organisms, including the mammalian muniscins, descendants of the TSET medium subunits. Thus, we have uncovered the machinery for an ancient and widespread pathway, which provides new insights into early eukaryotic evolution.

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Amino-acid sequence of the cytochrome-b5-like heme-binding domain from Hansenula anomala flavocytochrome b2

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1987.tb13642.x ◽

1987 ◽

Vol 169 (3) ◽

pp. 539-544 ◽

Cited By ~ 11

Author(s):

Pierre-Yves HAUMONT ◽

Marie-Antoinette THOMAS ◽

Francoise LABEYRIE ◽

Florence LEDERER

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Cytochrome B5 ◽

Binding Domain ◽

Heme Binding ◽

Flavocytochrome B2 ◽

Hansenula Anomala

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Tumor protein D54 defines a new class of intracellular transport vesicles

The Journal of Cell Biology ◽

10.1083/jcb.201812044 ◽

2019 ◽

Vol 219 (1) ◽

Cited By ~ 5

Author(s):

Gabrielle Larocque ◽

Penelope J. La-Borde ◽

Nicholas I. Clarke ◽

Nicholas J. Carter ◽

Stephen J. Royle

Keyword(s):

Membrane Trafficking ◽

Intracellular Transport ◽

Super Resolution ◽

Molecular Heterogeneity ◽

Rab Gtpases ◽

New Class ◽

Transport Vesicles ◽

Transport Vesicle ◽

Membrane Compartment ◽

Generic Class

Transport of proteins and lipids from one membrane compartment to another is via intracellular vesicles. We investigated the function of tumor protein D54 (TPD54/TPD52L2) and found that TPD54 was involved in multiple membrane trafficking pathways: anterograde traffic, recycling, and Golgi integrity. To understand how TPD54 controls these diverse functions, we used an inducible method to reroute TPD54 to mitochondria. Surprisingly, this manipulation resulted in the capture of many small vesicles (30 nm diameter) at the mitochondrial surface. Super-resolution imaging confirmed the presence of similarly sized TPD54-positive structures under normal conditions. It appears that TPD54 defines a new class of transport vesicle, which we term intracellular nanovesicles (INVs). INVs meet three criteria for functionality. They contain specific cargo, they have certain R-SNAREs for fusion, and they are endowed with a variety of Rab GTPases (16 out of 43 tested). The molecular heterogeneity of INVs and the diverse functions of TPD54 suggest that INVs have various membrane origins and a number of destinations. We propose that INVs are a generic class of transport vesicle that transfer cargo between these varied locations.

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