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Chapter 13 : Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis

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Abstract:

This chapter provides an overview on respiratory cytochromes, heme proteins, heme biosynthesis and an inventory of heme proteins and heme synthesis enzymes in strain 168. Succinate:quinone oxidoreductase (SQR) in aerobic gram-negative bacteria, e.g., , and in mitochondria generally contains only one heme, and the membrane anchor consists of two polypeptides (SdhC and SdhD). Gram-positive bacteria seem to contain only membrane-anchored cytochrome c. This is explained by the view that cytochrome c functions at the outer side of the cytoplasmic membrane, and in gram-positive bacteria it would be lost from the cell if it was not anchored. The majority of terminal oxidases of oxygen-respiring organisms belong to the heme-copper oxidase superfamily. The combined results of several studies show that cytochrome aa is the most important terminal oxidase in aerobic exponentially growing cells. The chapter provides an overview of tetrapyrrole biosynthesis in , with intermediates and required gene products indicated. The and genes seem to be essential for growth, indicating a more general function of the ResB and ResC proteins in the cell than simply having a role in cytochrome c synthesis, since c-type cytochromes are not essential for growth.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 1
FIGURE 1

Types of heme found in . In the structure of heme B, the pyrrole rings are labeled according to the nomenclature of Fisher.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 2
FIGURE 2

Overview of aerobic respiratory pathways in strain 168. Solid arrows show known electron transfer pathways, and dashed arrows show tentative pathways.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 3
FIGURE 3

General structure, composition, and function of SQR in the cytoplasmic membrane, and a comparison of the enzyme in B. subtilis and E. coli. The membrane anchor of B. subtilis SQR consists of one polypeptide (SdhC) and two heme B. That of E. coli consists of two polypeptides (SdhC and SdhD) and one heme B. The diagrams in the lowet patt of the figute illustrate the thetmodynamics of the electron transfer from succinate to quinone at pH 7.0. The oxidation of succinate to fumarate coupled to the reduction of MK to menaquinol is an endergonic reaction (ΔG° = + 22 kJ/mol), whereas the reduction of ubiquinone is exetgonic (AG0 = —15 kJ/mol) (90, 107, 137). In B. subtilis, the electrochemical potential across the cytoplasmic membtane is apparently used as an energy source to drive the “uphill” electron transfer from the high potential proximal heme (bp) to the low potential distal heme (bD). Electron transfer from heme bD to MK is then thermodynamically “downhill.” + and — indicate the outer and inner sides of the cytoplasmic membrane, respectively.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 4
FIGURE 4

The -type cytochromes present in B. subtilis strain 168. All four cytochromes are membrane bound. The amino acid sequences of the heme C domains of CccA, CccB, and QcrC are very similar, probably reflecting domain swapping during evolution. The heme C domain of CtaC is different from that of the other three cytochromes but very similar to that of cytochrome from several Bacillus species ( ). + and — indicate the sidedness of the cytoplasmic membrane (see legend to Fig. 3 ). n.d. indicates that no data are available. The two black dots in CtaC indicate a dicopper center, Cu- The redox potential indicated with an asterisk is that for the PS3 cytochrome ( ). Physicochemical data and sequence information for the . cytochromesare found in references , and .

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 5
FIGURE 5

Schematic presentation of the different types of terminal oxidases present in bacteria of the genus The subunits of the various terminal oxidase complexes are designated according to the names of the corresponding genes: cytochrome (Cta), cytochrome (Qox), cytochrome (Cba), cytochrome (Cyd), and cytochrome -2 (Cbd). The different types of heme prosthetic groups (heme A, B, C., D, or O) are indicated as a square. Black dots represent copper centers of the heme-copper oxidases (1 dot = Cu; 2 dots = Cu). The H/e stoichiometry for cytochrome (Cba) is approximately 1.5 ( ).

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 6
FIGURE 6

Schematic presentation of bacterial cytochrome P450 monooxygenase systems. Two different systems for the transfer of electrons from a reduced pyridine nucleotide to cytochrome P450 are known. (A) In most bacteria, a flavoprotein reductase (ferredoxin reductase) transfers electrons to an iron-sulfur protein (ferredoxin), which in turn delivers the electrons to P450. (B) The CYP102 flavocytochromes are self-sufficient fatty acid monooxygenases consisting of a flavin adenine dinucleotide (FAD), a flavin mononucleotide (FMN) and a heme-containing domain linked together in a single polypeptide. BioI, CYP107J, CYP134A1, CYP107K1, and CYP109B1 probably use an electron transfer system of the type shown in panel A.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 7
FIGURE 7

Heme synthesis pathways in strain 168. Intermediates and gene products are presented. Dashed arrows indicate that the genes and proteins involved in the pathway have not been identified.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Image of FIGURE 8
FIGURE 8

Organization of genes for uroporphyrinogen III and siroheme synthesis from glutamyl-tRNA in the chromosome of and other gram-positive bacteria. The sizes of the genes are not drawn exactly to scale. The gene cluster in is included for comparison. Gene products with similarity to the CysG precorrin-2 dehydrogenase and sirohydrochlorin fer-rochelatase domain and the Cys transmethylase domain are indicated in black and gray, respectively. See the text and Table 3 for more details. References: ( ); ( ); ( ); ( ); ( ); ( ); (prerelease of the genome sequence by Genome Therapeutics Corporation); ( ).

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
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Tables

Generic image for table
TABLE 1

Heme proteins in subtilis strain 168 identified experimentally or inferred from the genome sequence

A question mark indicates that the type of heme has not been determined experimentally.

Only the structural genes for the respective heme protein are indicated.

The proteins and genes encoding P450 of unknown function in are named according to the systematic P450 nomenclature ( ). For example, cyp102A3 is the gene encoding CYP102A3.

strain W23 contains a P450 gene (cypl09Al or ORF405) without correspondence in strain 168 ( ).

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
Generic image for table
TABLE 2

Properties of terminal oxidases found in species

The occurrence in species of several different cytochromes which can bind carbon monoxide and could represent terminal oxidases have been reported ( ). These tentative terminal oxidases have been named cytochrome ο (for oxidase). In its original meaning, the name cytochrome ο was intended to describe function and not heme composition ( ). Since the discovery of heme Ο ( ) ( Fig. 1 ), cytochrome ο has also been used to indicate that heme Ο is present in a particular cytochrome, e.g., cytochrome bo3. Wild-type cells have no heme O-containing cytochromes ( ). However, it has been shown that, depending on the growth conditions, one of the heme sites in cytochrome oxidase of PS3 and in cytochrome of can incorporate either heme A or heme Ο ( ).

The molecular mass of the unprocessed precursor polypeptide is based on the translated DNA sequence of cytochrome and cytochrome and of B. cytochrome and B. cytochrome -2.

The N-terminal segments of QoxA and CtaC have the features of typical lipoprotein signal sequences, and CtaC has been confirmed to bc a lipoprotein ( ).

strain 168; B, anthracis; C., D, haloaurans; E, OF4; F, stearot/iermophilus.

By analogy with cytochrome bd, heme b (low spin) may bc located in subunit 1, and heme (high spin) and may bc ligated between CydA and CydB.

Reference .

is as yet no spectral evidence for the presence of this heme

apparently contains two cytochrome enzymes, both related to B. stearothermophilus CbdAB.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13
Generic image for table
TABLE 3

Genes and proteins for heme biosynthesis in strain 168

Position on the calculated 360° chromosomal map.

A question mark indicates that the function of the protein is not established.

Mass of protein as predicted from the DNA sequence.

Citation: von Wachenfeldt C, Hederstedt L. 2002. Respiratory Cytochromes, Other Heme Proteins, and Heme Biosynthesis, p 163-179. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch13

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