Báo cáo khoa học: Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?

Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?

Tác giả: James W. A. Allen, Andrew P. Jackson, Daniel J. Rigden, Antony C. Willis, Stuart J. Ferguson, Michael L. Ginger

Lĩnh vực: Biochemistry, Molecular Biology, Evolutionary Biology

Nội dung tài liệu:
Nghiên cứu này khám phá sự đa dạng và tiến hóa của các hệ thống sinh tổng hợp cytochrome c loại c trong ty thể của sinh vật nhân thực. Các tác giả sử dụng dữ liệu sinh hóa, tin sinh học bộ gen so sánh và cấu trúc để cung cấp một cái nhìn toàn diện. Bài viết phân tích sự phân bố tiến hóa của ba con đường chính trong quá trình trưởng thành cytochrome c loại c ở ty thể, bao gồm hệ thống Ccm và enzyme heme lyase. Nghiên cứu cũng chỉ ra sự tồn tại của một con đường thứ ba, đặc trưng cho một số loài Trypanosomatida, gắn heme vào cytochrome c loại c có một gốc cysteine duy nhất trong motif gắn heme.

Mục lục chi tiết:

• Review Article
• Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?
• Keywords
• Mitochondrial cytochromes c and c₁ are present in all eukaryotes that use oxygen as the terminal electron acceptor in the respiratory chain. Maturation of c-type cytochromes requires covalent attachment of the heme cofactor to the protein, and there are at least five distinct biogenesis systems that catalyze this post-translational modification in different organisms and organelles.
• In this study, we use biochemical data, comparative genomic and structural bioinformatics investigations to provide a holistic view of mitochondrial c-type cytochrome biogenesis and its evolution.
• There are three pathways for mitochondrial c-type cytochrome maturation, only one of which is present in prokaryotes.
• We analyze the evolutionary distribution of these biogenesis systems, which include the Ccm system (System I) and the enzyme heme lyase (System III).
• We conclude that heme lyase evolved once and, in many lineages, replaced the multicomponent Ccm system (present in the proto-mitochondrial endosymbiont), probably as a consequence of lateral gene transfer.
• We find no evidence of a System III precursor in prokaryotes, and argue that System III is incompatible with multi-heme cytochromes common to bacteria, but absent from eukaryotes.
• The evolution of the eukaryotic-specific protein heme lyase is strikingly unusual, given that this protein provides a function (thioether bond formation) that is also ubiquitous in prokaryotes.
• The absence of any known c-type cytochrome biogenesis system from the sequenced genomes of various trypanosome species indicates the presence of a third distinct mitochondrial pathway.
• Interestingly, this system attaches heme to mitochondrial cytochromes c that contain only one cysteine residue, rather than the usual two, within the heme-binding motif.
• The isolation of single-cysteine-containing mitochondrial cytochromes c from free-living kinetoplastids, Euglena and the marine flagellate Diplonema papillatum suggests that this unique form of heme attachment is restricted to, but conserved throughout, the protist phylum Euglenozoa.
• Abbreviations
• Structures of (A) heme (Fe-protoporphyrin IX) and (B) heme bound to a polypeptide chain as in a typical c-type cytochrome, in which the vinyl groups of the heme are saturated by the addition of cysteine thiols that occur in a Cys-Xxx-Xxx-Cys-His motif (only the sulfur atoms of the cysteines are shown), forming covalent bonds between heme and protein. (C) Cartoon representation of heme attachment to protein in mitochondrial cytochrome c.
• Multiple pathways for heme cysteine attachment
• The c-type cytochromes are characterized by the covalent attachment of heme to the apocytochrome through thioether (carbon-sulfur) bonds (Fig. 1).
• Numerous examples of distinct c-type cytochromes have been described in Bacteria and, more recently, in some Archaea, where they typically function in electron transfer or at the catalytic sites of certain enzymes [2-9].
• However, the best known examples from the c-type cytochrome family are mitochondrial cytochromes c and c₁, which function as essential electron transfer components of the respiratory chain [7,8,10].
• The covalent attachment of two vinyl groups from the heme cofactor to the thiols in the CXXCH heme-binding motif of apocytochromes c is chemically far from facile (X is any amino acid, except cysteine), and there are multiple systems which catalyze this post-translational modification in biology [2,4,11-15].
• Systems I and II are modular and widely distributed amongst bacteria [2,4,6,12,14]; they have been studied using a combination of genetic and biochemical approaches [2,4,14,16,17].
• System I is understood best in Escherichia coli, where it consists of eight dedicated essential proteins, named CcmA-H (Fig. 2A), and a number of accessory proteins.
• CcmA-H are all membrane anchored or integral membrane proteins, and collectively function in the periplasm.
• The biogenesis of c-type cytochromes is a spatial and temporal problem; in bacteria, both heme and apoprotein are synthesized in the cytoplasm and must be transported to the periplasm, where heme attachment occurs.
• The apocytochrome polypeptide is translocated by the general type II secretion (Sec) proteins [18].
• How heme is transported remains an intriguing mystery.
• CcmA and CcmB are reminiscent of an ATP-dependent (ABC-type) transporter, and CcmA has been shown to hydrolyze ATP [19].
• However, no transport substrate has yet been identified; heme has been proposed, but much evidence weighs against this possibility [19-22].
• A more recent hypothesis is that CcmA and CcmB are required to release heme from the heme chaperone CcmE by coupling the free energy gained from ATP hydrolysis [21].
• CcmE is a key player in the Ccm system; it binds heme covalently as an intermediate in the cytochrome c biogenesis pathway [23].
• This remarkable heme attachment occurs between a histidine residue and a heme vinyl group.
• Heme attachment to CcmE is dependent on CcmC [24], an integral membrane protein with a number of interesting phenotypes arising from mutation in ccmC, some of which may be unrelated to c-type cytochrome biogenesis [25].
• CcmD is a very small (~60 amino acids) integral membrane protein that mediates complex formation between CcmC and CcmE [26].
• CcmF and CcmH are implicated in the transfer of heme from holo-CcmE to apocytochrome c, including the covalent heme attachment step to produce the product holocytochrome.
• E. coli CcmH is a fusion protein which includes the proteins known as CcmH and CcmI in many bacteria.
• CcmG is a thioredoxin-like protein [27] that forms part of an electron transfer chain.
• Electrons are transferred from the cytoplasmic protein thioredoxin, via the multidomain membrane protein DsbD, to CcmG, and then to the apocytochrome to reduce a disulfide bond that forms between the cysteines of the apocytochrome CXXCH heme-binding motif; these thiols must be reduced for heme attachment to occur (reviewed in [2]).
• Such a reductive pathway is thought to be necessary in E. coli, partly because the periplasm contains the strong, indiscriminate, disulfide-oxidizing protein DsbA.
• System II (Fig. 2B) is less well understood than System I at the molecular level, but it seems very likely to consist of four proteins [28].
• Cytochrome c biogenesis systems found in bacteria.
• Evolution of mitochondrial cytochrome c maturation
• System III for cytochrome c maturation consists of a single primary component, the enzyme heme lyase, which is found only in the mitochondrial intermembrane space (IMS) of animals, fungi and some protists [11,32].
• At least in fungi, heme lyase is supplemented by the flavoprotein Cyc2, which is thought to provide reducing equivalents for the heme attachment process [33].
• The biochemical study of heme lyase has proved challenging, and the molecular details of its enzymology are still largely unclear.
• Finally, a distinctive example of a biogenesis system that is required for the dedicated maturation of a particular substrate is provided by the recent description of System IV for cytochrome c maturation.
• Heme is attached through a single thioether linkage to cytochromes b₆ and b from the b₆f and bc₁ complexes of oxygenic phototrophs (cyanobacteria, plants, algae) and certain Bacillus species, respectively [34,35].
• The mechanism by which covalent heme attachment to Bacillus cytochrome b occurs is not yet known, but the identification of gene products from the green alga Chlamydomonas reinhardtii that restore cytochrome b₆ formation in four cch mutants constitutes the initial step in the characterization of System IV, which appears to be conserved in all oxygenic phototrophs [36].
• In species from the phylum Euglenozoa, which includes Euglena gracilis and the medically relevant trypanosomatids (Trypanosoma brucei, T. cruzi and pathogenic Leishmania species), heme is uniquely attached to the mitochondrial c-type cytochromes by a single thioether bond within a F/AXXCH heme-binding motif [37-41].
• In an earlier study, we determined that, in the trypanosomatids, the occurrence of single-cysteine-containing mitochondrial cytochromes c and c₁ correlates with the absence from both nuclear and mitochondrial genomes of genes encoding any component of the known c-type cytochrome maturation systems; we also provided experimental evidence that, for the single-cysteine-containing T. brucei cytochrome c, spontaneous (i.e. uncatalyzed) maturation is unlikely [41].
• These results indicate that at least one further pathway for cytochrome c maturation awaits discovery in the trypanosomatids.
• In this article, we draw on the resources that are provided through the availability of numerous complete genome sequences and several ab initio modeling programs.
• We consider in detail the evolutionary distribution of the machinery for mitochondrial cytochrome c assembly throughout the Eucarya, and the possible origins of heme lyase.
• Although the origin of the exclusively eukaryotic heme lyase remains mysterious, replacement of a proto-mitochondrial System I pathway for c-type cytochrome maturation occurred multiple times during protist evolution.
• With rare exceptions, these replacements probably occurred as a result of eukaryote-to-eukaryote lateral gene transfer (LGT) or endosymbiotic gene transfer of heme lyase.
• We also approach defining the limits of the distribution of the single-cysteine heme-binding motif found in some mitochondrial cytochromes c.
• Mapping character traits onto a consensus view of eukaryotic phylogeny
• The origin of the first eukaryotic cell has been debated for many years; during the 1980s and early 1990s, the available experimental evidence was generally consistent with an evolutionary model (called the Archezoa theory), which posited two early phases to eukaryotic evolution: an ancestral phase, in which the hallmark features of the eukaryotic cytoskeleton, endomembrane system and nucleus were evolved, followed by the second critical phase, which saw the acquisition of the α-proteobacterial endosymbiont and the evolution of the proto-mitochondrion.
• Although the results from some phylogenetic analyses conflicted with the model formulated by Cavalier-Smith (discussed in [42]), the Archezoa theory generally received robust support in phylogenetic trees derived from the analysis of small subunit rRNA or translation elongation factor proteins.
• Grouped at the base of many of these trees were several eukaryotic lineages, including diplomonads (represented by Giardia), the parabasalids (represented by Trichomonas) and the Microsporidia [43,44] (and reviewed recently in [45,46]).
• The distinctive ultrastructure of these organisms suggested that they apparently possessed neither mitochondria nor other hallmark eukaryotic organelles, such as peroxisomes and golgi, and their status as Archezoa denoted that they were believed to be ancestrally without these organelles.
• We now know that this is not the case; more recent phylogenetic treatments have resulted in the repositioning of at least some formerly basal or ‘primitive’ eukaryotes elsewhere within the eukaryotic tree [46-48].
• Furthermore, although the secondary loss of peroxisomes has occurred numerous times in evolution, the aforementioned organisms crucially retain mitochondria, golgi and other classically eukaryotic subcellular compartments that have merely been remodeled beyond obvious or easy recognition [49–53].
• Thus, there are no known examples of contemporary eukaryotes that lack double-membrane-bound organelles of mitochondrial descent; indeed, although difficult to prove, a popular current viewpoint is that the acquisition of the proto-mitochondrial endosymbiont could have been coincident with eukaryotic origins (see, for example, [47,54] for a further discussion).
• Although the position of the root for eukaryotic evolution remains a contentious issue – Cavalier-Smith has argued that the last common ancestor of all extant eukaryotes diverged with the unikont-bikont split (Fig. 3) [55-57]; other results have suggested that it is still not possible to discount a previously long-standing view that the diplomonads and parabasalids belong to the earliest diverging eukaryotic lineage [46,47,58] comparative interrogations of various morphological and molecular character traits, as well as phylogenies based on the analysis of multiple gene sets, have resulted in a seemingly robust resolution of eukaryotic diversity into six major groupings ([59] and reviewed in [46,47,60,61]).
• The framework provided by this resolution is increasingly being used to inform on the evolution of various fundamental aspects of eukaryotic biology, both within and between these major groupings [55-57,62-66].
• It is this consensus view of eukaryotic evolution on which the comparative analysis described below is based.
• A phylogeny for mitochondrial c-type cytochrome maturation
• Using the complete or draft nuclear and mitochondrial genome sequences indicated in supplementary Doc S1, we mapped the distribution of mitochondrial cyto-chrome c maturation pathways onto a consensus view of eukaryotic phylogeny (Fig. 3).
• Our aim was to assess whether there was any obvious order to the otherwise mosaic distribution of mitochondrial cyto-chrome c biogenesis machineries that has previously been hinted at [67,68].
• The presence of the Ccm system in higher plants and some unicellular eukaryotes [e.g. the deeply divergent jakobid Reclinomonas americana, ciliates and the rhodophyte (red alga) Cyanidioschyzon merolae] has been described previously [69-74], whereas other eukaryotes, such as the animals, the chlorophyte green alga C. reinhardtii and the malarial parasite Plasmodium falciparum (an apicomplexan) have heme lyase for maturation of mitochondrial cytochromes c [2,15,32,75-77].
• The mitochondrial genome sequences of various excavate, algal, plant and ciliate taxa very clearly point to the presence of System I within the α-proteobacterial endosymbiont from which mitochondria evolved [69,70,72,78,79].
• However, taking into account the generally robust support for relationships within and between the taxonomic groups shown in Fig. 3, our comparative genomic analysis can be used to provide new insight into the evolution of mitochondrial cytochrome c maturation.
• Observations that are key to the discussion that follows in subsequent sections are: (a) there is no evidence for the occurrence of heme lyase within the bikont supergroup Excavata; (b) in the unikonts, heme lyase is the only c-type cytochrome maturation system present; (c) there is a mosaic distribution of the Ccm system and heme lyase within the Chromoalveolata and Plantae; (d) wherever the multicomponent Ccm system is used for mitochondrial cytochrome c maturation, it is always partially encoded on the mitochondrial genome; this is perhaps unsurprising given that CcmC and CcmF are mitochondrial integral membrane proteins containing multiple predicted transmembrane helices.
• The phylogenetic distribution of the different pathways used for mitochondrial c-type cytochrome maturation in eukaryotes.
• Key to the symbols used (reading from left to right):
• Heme lyase (c/c₁), Heme lyases (c + c₁), Ccm system, Ccm system (as evidenced from mito genome sequence), Ccm system absent (as evidenced from mito genome sequence), Degenerate mitochondria which do not contain c-type cytochromes, No known maturation system present, Containing c-type cytochromes with an atypical heme-binding motif
• The mitochondrial genome sequence is complemented by the availability of a complete or draft nuclear genome sequence for the same organism, the following always holds true: (i) if components of the Ccm system are encoded in the mitochondrial genome, further dedicated Ccm components are also encoded in the nuclear genome; (ii) there are no examples of eukaryotes possessing multiple systems for mitochondrial cyto-chrome c maturation.
• Thus, even without the availability of a sequenced nuclear genome, the absence from a protozoan or algal mitochondrial genome of genes encoding Ccm components almost certainly provides a reliable indication that System I will not be used for the maturation of mitochondrial cytochromes c and c₁.
• There are several green, red (rhodophyte) and chromist algae (belonging to the Chromalveolata), plus other protozoan species (the amoebozoan Acanthamoeba cas-tellanil), for which no nuclear genome sequence is available, but there is an accessible or annotated [79] mitochondrial genome sequence on which no compo-nent of the Ccm system is encoded.
• Similarly, there is extensive sequence coverage for the uniquely