Growth phenotype analysis of heme synthetic enzymes in a halophilic archaeon, Haloferax volcanii

Kosugi, Naoki; Araki, Takuma; Fujita, Junpei; Tanaka, Satoru; Fujiwara, Taketomo

doi:10.1371/journal.pone.0189913

Cited by 6 publications

(2 citation statements)

References 36 publications

(68 reference statements)

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“…Coproheme decarboxylase (ChdC, formerly HemQ) is a key element in the coproporphyrin-dependent heme biosynthetic pathway of mainly monoderm, but also some diderm, archaea, and intermediate bacteria. − In fact, it catalyzes the decarboxylation of the two propionate groups at positions 2 and 4 of iron-coproporphyrin III (coproheme) to form heme b . Many recent publications have elucidated the physiological role of ChdC, ,, but its structure–function relationship is still not completely understood.…”

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confidence: 99%

Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes

et al. 2018

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Coproheme decarboxylases (ChdC) catalyze the hydrogen peroxide-mediated conversion of coproheme to heme b. This work compares the structure and function of wild-type (WT) coproheme decarboxylase from Listeria monocytogenes and its M149A, Q187A, and M149A/Q187A mutants. The UV–vis, resonance Raman, and electron paramagnetic resonance spectroscopies clearly show that the ferric form of the WT protein is a pentacoordinate quantum mechanically mixed-spin state, which is very unusual in biological systems. Exchange of the Met149 residue to Ala dramatically alters the heme coordination, which becomes a 6-coordinate low spin species with the amide nitrogen atom of the Q187 residue bound to the heme iron. The interaction between M149 and propionyl 2 is found to play an important role in keeping the Q187 residue correctly positioned for closure of the distal cavity. This is confirmed by the observation that in the M149A variant two CO conformers are present corresponding to open (A0) and closed (A1) conformations. The CO of the latter species, the only conformer observed in the WT protein, is H-bonded to Q187. In the absence of the Q187 residue or in the adducts of all the heme b forms of ChdC investigated herein (containing vinyls in positions 2 and 4), only the A0 conformer has been found. Moreover, M149 is shown to be involved in the formation of a covalent bond with a vinyl substituent of heme b at excess of hydrogen peroxide.

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Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes

et al. 2018

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“…Hfx. volcanii was shown to use AhbD under anaerobic conditions and ChdC under aerobic conditions [ 162 ].…”

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confidence: 99%

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Pfeiffer

Dyall‐Smith

2021

Genes

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Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

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Biosynthesis and Insertion of Heme

Müller¹,

Mingers²,

Haskamp³

et al. 2018

Aerobic Utilization of Hydrocarbons, Oils and Lipids

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Growth phenotype analysis of heme synthetic enzymes in a halophilic archaeon, Haloferax volcanii

Cited by 6 publications

References 36 publications

Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes

Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Biosynthesis and Insertion of Heme

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