Evolution of the Cytochrome-Bd Type Oxygen Reductase Superfamily and the Function of Cydaa' in Archaea Abstract Introduction

bioRxiv preprint doi: https://doi.org/10.1101/2021.01.16.426971; this version posted January 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

1 Evolution of the cytochrome-bd type oxygen reductase superfamily and the

2 function of cydAA’ in Archaea

3 Ranjani Murali1*, Robert B. Gennis2, James Hemp3* 4 1Division of Biology and Biological Engineering, California Institute of Technology 5 2 Department of Biochemistry, University of Illinois, Urbana-Champaign 6 3School of Medicine, University of Utah 7 *Correspondence can be addressed to: [email protected], [email protected] 8 9 Abstract

10 Cytochrome bd-type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze

11 oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of

12 their biochemical diversity is unknown. Here we used phylogenomics to identify 3 families and several

13 subfamilies within the cytbd superfamily. The core architecture shared by all members of the superfamily

14 consists of four transmembrane helices that bind two active site hemes, which are responsible for oxygen

15 reduction. While previously characterized cytochrome bd-type oxygen reductases use quinol as an

16 electron donor to reduce oxygen, sequence analysis shows that only one of the identified families has a

17 conserved quinol binding site. The other families are missing this feature, suggesting that they use an

18 alternative electron donor. Multiple gene duplication events were identified within the superfamily,

19 resulting in significant evolutionary and structural diversity. The CydAA’ cytbd, found exclusively in

20 Archaea, is formed by the co-association of two superfamily paralogs. We heterologously expressed

21 CydAA’ from Caldivirga maquilingensis and demonstrated that it performs oxygen reduction with quinol

22 as an electron donor. Strikingly, CydAA’ is the first isoform of cytbd containing only b-type hemes

23 shown to be active when isolated, demonstrating that oxygen reductase activity in this superfamily is not

24 dependent on heme d.

25 Introduction

Murali et al. ISMEJ-21-00087A 1

26 The predominance of oxygen in our atmosphere determines the bioenergetic importance

27 of oxygen as an electron acceptor and the prevalence of aerobic respiratory chains. There are

28 only three enzyme superfamilies capable of acting as terminal respiratory oxygen reductases -

29 heme-copper oxygen reductases, alternative oxidases and cytochrome bd-type oxygen reductases

30 (cytbd)1. While enzymes from this superfamily have been characterized from a number of

31 Bacteria, their role in archaeal respiration has not yet been determined. Archaeal aerobic

32 respiratory chains share some similarities with bacterial respiratory chains, however they often

33 differ in their composition of respiratory enzymes and are adapted to use different cofactors such

34 as methanophenazine and F420. Complexes that are typically involved in bacterial respiration

2 3 35 such as succinate-quinone oxidoreductases , cytochrome bc1 complexes and heme-copper

36 oxygen reductases from archaea have been previously characterized4,5, while NADH:quinone

37 oxidoreductases and alternative complex III are absent from this domain6. The presence of

38 cytochrome bd-type oxygen reductases has been noted in archaeal genomes7, metagenomes and

39 metaproteomes8–11 but, no functional member of the cytbd superfamily in archaea has ever been

40 demonstrated.

41 Cytochrome bd-type oxygen reductase is a respiratory enzyme that converts oxygen to

42 water using three hemes, unlike the heme-copper oxygen reductases which have two hemes and

43 a copper in the active sites1. Purified cytbd accepts electrons from quinols using a low-spin heme

44 b558 and transfers these electrons to a di-heme active site containing two high-spin hemes. In

45 some of the characterized cytochrome bd enzymes, these active site hemes were shown to be

46 heme b595 and heme d, but some other isoforms were shown to contain only hemes b. Those

47 cytochrome bd family members that contain only hemes b are usually referred to as cyanide

48 insensitive oxidases (CIO) or cytochrome bb’–type oxygen reductase, and have been identified

Murali et al. ISMEJ-21-00087A 2

49 in Pseudomonas aeruginosa, Bacillus subtilis and others12–15. It is unclear whether the presence

50 of only hemes b has a physiological implication but it has been suggested that these enzymes are

51 less sensitive to inhibition by cyanide13. There is no sequence signature that distinguishes those

52 enzymes in the superfamily that only contain heme b. No CIO has ever been isolated and

53 characterized.

54 The canonical cytochrome bd oxygen reductases contain a minimum of two subunits,

55 cydA and cydB, but often contain additional “auxiliary” subunits 16–18 such as CydX, a single-

56 transmembrane subunit that is associated with cytochrome bd-I from E. coli that has been

57 implicated in the stability of the enzyme19. Cytochrome bd-type oxygen reductases have a high

58 affinity for oxygen20 and the previously characterized cytbds have been associated with roles in

59 oxygen detoxification, respiratory protection of nitrogenases and as part of sulfide oxidizing

60 respiratory chains21–25. Cytochrome bd catalytic turnover generates a proton motive force by

61 translocation of protons using a conserved proton channel from the cytoplasm to the site of

62 oxygen reduction located near the periplasmic side (electrically positive) of the membrane26. Yet,

63 cytochrome bd is not as energetically efficient as the heme-copper oxygen reductases which

64 pump protons in addition to translocating “chemical” protons from the cytoplasm to the

65 periplasmic active site27,28. Expression of cytochrome bd has often been associated with

66 microoxic conditions where a high-affinity oxygen reductase would be required29.

67 In this work, we used phylogenomics to determine the diversity and distribution of this

68 high affinity oxygen reductase in Archaea and Bacteria. We determined that there are three

69 distinct families of cytbd – one of which contained the quinol binding characteristics present in

70 the structures of cytbd from Escherichia coli and Geobacillus thermodenitrificans30–32 and two

71 which do not – and discussed their evolutionary relationships. The distribution of these families

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72 even within Archaea involve significant variation and include the two distinct isoforms CydAB

73 and CydAA’, the latter of which appears to have been created by gene duplication. We evaluate

74 the relative distribution of the CydAA’ and CydAB within the domain archaea and consider the

75 likely role of CydAA’ variants within their ecological context. In addition, we show that the

76 CydAA’ from Caldivirga maquilingensis is a highly active oxygen reductase with unique

77 biochemical and structural characteristics. This combined phylogenomic and experimental

78 approach has significantly expanded our knowledge of the evolutionary and biochemical

79 diversity within the superfamily, which has important implications for the role of the cytbd

80 superfamily in novel respiratory pathways.

81 Results

82 Diversity of cytochrome bd-type oxygen reductases

83 The molecular structures of cytochrome bd-type oxygen reductases from Escherichia coli

84 and Geobacillus thermodenitrificans have been determined, and showed that cytbd typically has

85 two conserved subunits cydA and cydB, along with a third subunit, cydX or cydS which is a

86 single transmembrane subunit that is not well conserved or found along with cydA and cydB in

87 the genome30–33. Of the two main subunits, cydA is better conserved in all known cytochrome

88 bd-type oxygen reductases while cydB is very divergent and is hypothesized to have evolved at

89 faster rates than cydA34. The cydA subunit is made of nine transmembrane helices and contains

90 almost all the conserved amino acids known to be important for catalyzing oxygen reduction and

91 proton translocation, including the ligands for three hemes and the residues forming a proton

92 channel35,36. The first four helices of cydA contain all of the amino acids that form the active site.

93 These include the proton channel and ligands to bind the active site heme b595 and heme d (these

Murali et al. ISMEJ-21-00087A 4

94 ligands have only been verified in the isoforms containing hemes b and d, and not the ones

95 containing only hemes b). The other five helices (V- IX) form the quinol binding site in the

96 biochemically characterized bd-type oxygen reductases and include the ligands to heme b558, the

97 point of entry for electrons from quinols30–32. With this structural framework in mind, we

98 performed a sequence analysis of cytochrome bd-type oxygen.

99 An analysis of 24706 genomes available in the Genome Taxonomy Database

100 (release89)37,38, revealed the presence of 17852 cydA homologs. Of these, 13007 genomes

101 contained at least one cydA homolog, suggesting that this enzyme family is widely distributed

102 and important (Supplementary Table1). Phylogenomic analysis of cydA homologs revealed 15

103 clades of cydA that could be distinguished on the basis of unique sequence characteristics.1

104 (Supplementary Figure S1, Supplementary Tables1,2). Four of these clades contain the

105 features that are considered part of the quinol binding site – for e.g., conserved residues Lys252,

106 Glu257 (E.coli cydA numbering) while the remaining do not. We inferred that the former four

107 cydA clades were quinol:O2 oxidoreductases and we named them qOR1, qOR2, qOR3 and

108 qOR4a. While cydA of the families qOR1, qOR2 and qOR3 associate with cydB to form cydAB,

109 cydAA’ is formed by the co-association of two distinct cydA clades, qOR4a and qOR4b. qOR4b

110 does not possess quinol binding site characteristics and is likely the result of a gene duplication

111 event. Phylogenetic clustering of cydA sequences from all 15 cydA clades demonstrated that 2 of

112 the remaining clades are missing quinol binding sites and instead contain a number of heme c

113 binding motifs (CxxCH) (Supplementary figure S1, Supplementary multiple sequence

114 alignments MSA1, MSA3). We named these enzymes OR-C1a and OR-C1b because of the

115 presence of heme c binding motifs. Similar to qOR4a/4b, the ‘a’ and ‘b’ attachment to the names

116 signifies that their genomic context suggests that they co-associate to form one enzyme OR-C1.

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117 Eight of the remaining cydA clades were related and named OR-N1, OR-N2, OR-N3a, OR-N3b,

118 OR-N4a, OR-N4b, OR-N5a and OR-N5b. OR-N is named for Nitrospirota because of

119 predominance of these enzymes in that phylum (Supplementary Figure S1, Supplementary

120 multiple sequence alignments MSA1, MSA2, MSA3). Their close relationship is also

121 supported by the likely structure of the proteins of which they are a part and their genomic

122 context (Figure 1). We have attempted to develop a nomenclature for the cytochrome bd-type

123 oxygen reductase family that can be easily expanded upon. We designate 3 large families of

124 cytochrome bd-type oxygen reductases – qOR, OR-C and OR-N - based on their phylogenetic

125 placement, presence/absence of biochemical signatures such as quinol and heme c binding site

126 features, genomic operon context and taxonomic origin. We have designated subfamilies

127 numerically starting from 1 and attached an ‘a’ or ‘b’ subscript if it is likely that two cydA

128 subfamilies co-associate to form one enzyme. Most of the ‘a’-type subfamilies include the proton

129 channel residues E99 and E107 (E. coli numbering) while ‘b’-type subfamilies do not. It appears

130 that ‘a’ and ‘b’-type subfamilies are also the result of multiple independent gene duplication

131 events within this superfamily. We will discuss the unusual number of gene duplication events

132 within the cytbd superfamily and the OR-C and OR-N families later in the text and in

133 Supplementary Material but begin with the quinol oxidizing qOR family. Sequences from this

134 family contain all the amino acids that were previously identified as forming the heme ligands,

135 proton channel, oxygen reduction site and quinol binding site30–32,36.

136 Evolution of the quinol-oxidizing cytochrome bd-type oxygen reductases (qOR)

137 To explore the evolutionary relationship between the families qOR1, qOR2, qOR3 and

138 qOR4a, which are true orthologs, we generated a maximum likelihood phylogenetic tree using

139 RAxML with the OR-C and OR-N family sequences as outgroup (Figure 2). Sequence features

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140 can be identified to distinguish these families and to validate the above identified monophyletic

141 clades as meaningfully distinct; some of which are outlined below while the remaining features

142 are mentioned in Supplementary Table 6. All cydA sequences from qOR1 subfamily have 7

143 amino acids between the two conserved glutamates in the proton channel Glu99 and Glu107 such

144 as in Escherichia coli cydA 26,39 while cydA sequences from qOR2, qOR3 and qOR4a typically

145 have 6 amino acids between the two conserved glutamates (ex. as between Glu101 and Glu108

146 in qOR3-subfamily cytbd from Geobacillus thermodenitrificans30). This insertion/deletion has

147 been hypothesized to lead to a reversal in the position of hemes from the qOR1-bd in

148 Escherichia coli to the qOR3-bd in Geobacillus thermodenitrificans although further research is

149 required to establish whether the reversal of heme positions is universal (further discussion on

150 the insertion/deletion in the proton channel and the Q-loop is included in Supplementary

151 Material). Sequence features which distinguish the qOR4a-subfamily cytbd are insertions

152 between helices V and VI, as well as insertions in helix VIII (Supplementary alignment MSA1,

153 Supplementary Table 6) Conserved tyrosines (Tyr115 and Tyr117 Geobacillus

154 thermodenitrificans cydA numbering) are present in qOR2 and qOR3 families but not in the

155 qOR4a-subfamily, which is consistent with the close evolutionary relationship between the

156 qOR2 and qOR3-subfamilies observed in the tree topology. Other conserved sequence features,

157 unique to each family are listed in Supplementary alignment MSA2 and Supplementary

158 Table 6.

159 Comparing the cydA phylogenetic tree and the distribution of cytochrome bd-type

160 oxygen reductases across Archaea and Bacteria provides some insight into the relative age of

161 these families. The qOR1 subfamily, which includes the Escherichia coli enzyme, at present

162 count seems to be the most widely distributed with enzymes in over 60 bacterial phyla,

Murali et al. ISMEJ-21-00087A 7

163 (Supplementary Table 2, 4) but it is only sparsely distributed in Archaea. In fact, there are only

164 a very few representatives in Euryarchaeota and Asgardarchaeota (Figure 2). It is only widely

165 distributed in Halobacterota, whose oxidative metabolism is expected to have evolved relatively

166 late40(Figure 3). This strongly suggests that the qOR1 subfamily is the oldest of the extant

167 families and that it is likely that cytochrome bd-type oxygen reductases originated in Bacteria.

168 While cydA from the qOR2 subfamily is also fairly well-distributed and found in over 20

169 bacterial phyla, the qOR3-subfamily enzymes are almost exclusive to the Firmicutes and

170 Firmicutes_I phyla with a few enzymes in Archaea. The qOR4a-subfamily enzymes appear to be

171 specific to the Archaea (Supplementary Tables 2, 4). A close evolutionary relationship between

172 the qOR2 and qOR3-subfamilies is suggested by cydA tree topology and identifiable sequence

173 characteristics but other trees we inferred have modelled a closer relationship between the qOR2

174 and qOR1 subfamilies (data not shown). Furthermore, the qOR1 subfamily has 7 amino acids

175 between the conserved glutamates in the proton channel, while the qOR4a, qOR2 and qOR3

176 subfamilies consistently have 6 amino acids. Lastly, enzymes from the qOR4a, qOR2 and qOR3

177 subfamilies are almost completely absent from Proteobacteria. This suggests that the qOR2,

178 qOR3 and qOR4a subfamilies diverged from the qOR1 family, Before proteobacteria diverged

179 from other bacterial phyla. While our dataset and phylogenetic analysis is consistent with the

180 above discussion, it must be noted that many lateral gene transfers have been observed within the

181 cytochrome bd-type oxygen reductase1 which complicate evolutionary analysis.

182 As mentioned above, most cydA subfamilies are widely distributed within Bacteria and

183 Archaea, but the qOR4a-subfamily is unique in having sequences that belong only to Archaea. In

184 addition, the qOR4a-subfamily is unique in having a completely different subunit II (cydA’),

185 while the qOR1-, qOR2- and qOR3- subfamily members appear to have cydB homologs as their

Murali et al. ISMEJ-21-00087A 8

186 subunit II. cydB is either not homologous to cydA’ or is evolutionarily distant. The unique

187 ancestry of the qOR4a-subfamily enzymes which is specific to archaea raises a question about its

188 distribution within that domain.

189 Distribution of cytochrome-bd type oxygen reductases in archaea

190 To investigate the distribution of cytochrome bd-type oxygen reductases within Archaea

191 and to contextualize the evolution of cydA within archaeal evolution, we mapped the presence of

192 qOR4a, qOR1, qOR2 and qOR3 subfamilies of cydA onto a phylogenetic tree of all archaea,

193 using a concatenated gene alignment made from the archaeal genomes in GTDB37 using

194 Anvi’o41, (Figure 2). It is clear from this representation that most of the qOR4a-subfamily or

195 cydAA’ belong to the class Thermoprotei within the phylum Crenarchaeota with a few cydAA’

196 in Nitrosphaeria, Thermoplasmatota and Archaeoglobi. Within the Thermoprotei, almost all

197 members of the order Thermoproteales contain cydAA’ and family Acidilobaceae contain

198 cydAA’ (Supplementary Table 3).

199 To place cydAA’ into an ecological context we looked at their environmental distribution

200 (Supplementary Table 5). Microbes containing cydAA’ are largely found in solfataric fields,

201 hot springs and deep-sea vents, suggesting that cydAA’ might only be utilized by thermophiles,

202 such as organisms from the genus Vulcanisaeta, Caldivirga, Thermofilum and Thermocladium42.

203 Within Yellowstone National Park (YNP), a number of these genera are found in hypoxic,

204 sulfur/iron-rich ecosystems, although Pyrobaculum and Thermofilum have also been found in

205 more oxygenated environments. It has been suggested that members of the Thermoproteales

206 which are found in aerobic environments have a heme-copper oxygen reductase and are more

207 likely to be using aerobic respiration as their primary energetic pathway42. This is consistent with

208 what we observe in Thermoproteales – organisms which do not have cydAA’ have heme-copper

Murali et al. ISMEJ-21-00087A 9

209 oxygen reductases instead (Supplementary Table 3). However, of the 8 Pyrobaculum genomes

210 in the GTDB database, the three genomes that have cydAA’, but are missing a heme-copper

211 oxygen reductase are capable of aerobic respiration43,44. This is suggestive of an adaptation based

212 on oxygen availability in the environment resulting in a trade-off between the greater energetic

213 efficiency and higher oxygen affinity of HCOs and bd respectively20,28.

214 Expression of the cydAA’ genes have been demonstrated in the hot springs and sulfur-

215 rich/iron-rich environments within Yellowstone National Park, using RT-PCR10 and

216 metatranscriptomics (Table 1). While the hot springs were typically hypoxic and sulfur-rich, the

217 iron oxide mats had higher oxygen concentration at the surface and had <0.3 μM concentrations

218 of O2 within 1 mm. Nitrosphaeria, Acidilobaceae, Thermoproteales and Thermoplasmatota

219 expressed cydAA’ in these environments, however it is not clear whether these microorganisms

220 were exposed to high O2 concentrations. In fact, the Acidolobaceae are expected to be found in

10,45 221 the middle and bottom layers of this mat where O2 concentrations are lower . All of the above

222 observations are consistent with the presence of cydAA’ in microaerobic and hypoxic

223 environments. The obvious question that needed to be addressed is whether cydAA’ actually

224 functions as an oxygen reductase. This was accomplished by biochemically characterizing the

225 CydAA’ from C. maquilingensis.

226 Partial purification and spectroscopic characterization of the cydAA’ from C.

227 maquilingensis

228 The cydAA’ operon from Caldivirga maquilingensis consists of two genes – cydA and

229 cydA’. There are no additional subunits encoded within the operon corresponding to cydX/cydY

230 or cydS, which are associated, respectively, with E.coli cydAB and G.thermodenitrificans

231 cydAB. Homologues of these subunits are not apparent in the C. maquilingensis genome. We

Murali et al. ISMEJ-21-00087A 10

232 cloned the operon into the pET22b vector and expressed it in an Escherichia coli strain in which

233 both bd-I and bd-II were deleted (CBO - C43, ΔcydA ΔappB)17. The enzyme, cytochrome bb’

234 oxygen reductase from Caldivirga was engineered to have numerous different tags –

235 6xHistidine, FLAG, GST and GFP. None of these tags were successful, either because of a poor

236 yield of protein or because of the inability of the affinity-tagged proteins to bind to columns with

237 their corresponding epitopes. A GFP-tagged protein was used to verify the expression in E.coli

238 of CydAA’ from Caldivirga maquilingensis. The presence of the protein could be observed by

239 following the fluorescence of the protein under UV light. Since subunit II was tagged with GFP,

240 it confirms the presence of subunit II in the preparation (Supplementary Figure 3). In addition,

241 the purified protein was verified by mass spectrometry with many peptides recovered from

242 subunit I. (Supplementary Figure 4). Gel electrophoresis of a partially purified CydAA’ shows

243 two bands of the sizes expected for CydA and CydA’ (Supplementary Figure 5).

244 A UV-visible spectrum of CydAA’ in the reduced-minus-oxidized state reveals the

245 absence of the heme d absorbance peak. The presence of heme b595 is also not apparent in the

246 spectrum since the maxima at 595 nm and the Soret peak at 440 nm are also missing. This could

247 indicate that heme b595 is low spin in this preparation. Hemes were extracted from CydAA’ of

248 Caldivirga maquilingensis as described previously46. Only b-type hemes are present in the

249 enzyme (Figure 4). This was verified by analyzing the hemes in the protein by LC-MS (data not

250 shown).

251 CydAA’ from Caldivirga maquilingensis has oxygen reduction activity

252 The oxygen reduction activity of CydAA’ was tested using a Clark electrode, with

253 reduced coenzyme Q1 (reduced using DTT) as the electron donor. (Table 2, Figure 4) At 37 ŀ

254 the specific activity is ~330 e-/s (/heme b). While this is not as high as the activity of E. coli bd at

Murali et al. ISMEJ-21-00087A 11

255 the same temperature (over 1000 e-/s), the enzymatic activity is substantial, particularly

256 considering the fact that the source of the enzyme is a thermophilic organism whose growth is

257 optimum at 65 ŀ. The oxygen reductase activity of CydAA’ is insensitive to the presence of 250

258 µM KCN, a concentration of cyanide that would completely inhibit the activity of heme-copper

259 oxygen reductases1. Since CydAA’ was expressed in the bd-deletion mutant, E.coli strain CBO,

47 260 the only other potential oxygen reductase in this preparation is bo3 ubiquinol oxygen reductase

261 so the lack of cyanide sensitivity confirms that our purification protocol has separated the two

262 enzymes. The enzyme is also susceptible to Aurachin AC1-10, a known inhibitor of cytochrome

263 bd at concentrations as low as 250 nM48. We did not test for other possible functions for cydAA’

264 such as catalase activity49 or peroxidase activity50.

265 We previously noted that cydAA’ is typically found in organisms that perform sulfur-

266 based chemistry such as sulfur reduction and sulfate reduction (Supplementary Table 5) and

267 use DMSO-reductase like enzymes which use molybdopterin as a cofactor10. Combining the

268 above observation with the demonstrated oxygen reductase activity of CydAA’, it is likely that

269 the role of CydAA’ is to detoxify oxygen to protect oxygen-sensitive enzymes involved in sulfur

270 metabolism. This is similar to its expected role in Desulfovibrio24 and in the protection of

271 nitrogenases during the process of nitrogen fixation22.

272 It is striking that oxygen reduction is conserved in the qOR4a-subfamily despite the

273 replacement of CydB with CydA’ and therefore, it is worth considering the similarities and

274 differences between E.coli CydAB and C.maquilingensis CydAA’.

275 Structural differences between CydAB and CydAA’ inferred from homology models

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276 To aid in the understanding of differences between CydAA’ and other CydAB, we used

277 multiple sequence alignments (Supplementary Figure 2) and structural models of cydA and

278 cydA’ from Caldivirga maquilingensis (Supplementary Figure 7, pdb files are available in

279 supplementary material). The most drastic difference between the E.coli and C.maquilingensis

280 enzymes is the absence of cydB. cydB in E.coli was shown to contain the oxygen diffusion

281 channel31,32 and an additional proton channel leading to heme d, bound to subunit I30–32. In C.

282 maquilingensis the second subunit is cydA’ which is 26 % similar to cydA. Only the first two

283 helices are well conserved between these subunits in C. maquilingensis whereas other qOR4a-

284 type cydA’ and qOR4b-type cydA, such as in A. fulgidus are similar in the first 4 helices. To

285 substitute for the proton channel that exists in cydB, conserved residues in cydA’ such as Thr71,

286 Thr74 and His126 might form a different proton channel. cydA’ probably hosts an oxygen

287 diffusion channel to substitute for the loss of the one in cydB but it is not possible to tell from the

288 sequence alignment or structural model where in the subunit this might be. Interestingly, cydA’

289 retains His19 which has been implicated as a ligand to heme d and heme b595 in E. coli and G.

290 thermodenitrificans cytbd respectively, which might suggest that an additional heme might bind

291 to the cydA’ subunit but we cannot verify or refute this from our protein preparation. A number

292 of mutations are observed around the binuclear-active site in subunit I, which might affect the

293 midpoint potential of the heme or the proton-coupled electron transfer mechanisms.

294 Evolution of cydA’ and other cydA homologs missing the quinol binding site

295 As mentioned earlier, a phylogenomic analysis of cydA homologs revealed two new

296 families, OR-C and OR-N that share the first four helices containing the oxygen reduction site.

297 The cydA subunit of OR-C bd-type oxygen reductases typically has eight transmembrane helices

298 and an extended C-terminal periplasmic portion that binds hemes c, strongly suggesting that a

Murali et al. ISMEJ-21-00087A 13

299 cytochrome c could be an electron donor to this family. Adjacent to the OR-C1a-type cydA is

300 OR-C1b which also has 8 transmembrane helices. The OR-N3a/b, -N4a/b and -N5a/b family

301 cydA typically have 10 helices while the OR-N2 and -N1 have 14 transmembrane helices. OR-N

302 enzymes have been previously noted in Nitrospira51 and Chloroflexi (N5a/b)52. They were

303 recently shown to be expressed in manganese oxidizing autotrophic microorganism, Candidatus

304 manganitrophus noduliformans (N2/N1)from the phylum Nitrospira53 and is implicated in

305 oxygen reduction. Greater details on the OR-C and OR-N families, including distribution,

306 alignments and conserved amino acids are found in Supplementary Material. The OR-C and

307 OR-N families are widely distributed in Bacteria. OR-C is present only in Bacteria, while OR-N

308 has very few representatives in Archaea (Supplementary Table 2, Supplementary Table 4).

309 A phylogenetic tree of all cydA clades suggest that the OR-C and OR-N families are

310 more closely related to qOR4b than the other qOR subfamilies (Figure 1). There are also

311 conserved sequence features that suggest that the OR-C and OR-N families are more closely

312 related to the qOR3 and qOR4a families than the qOR1 family including the deletion in the

313 proton channel between the conserved glutamates E101 and E108 like in G.thermodenitrificans

314 cytbd, and the presence of nearby conserved tyrosines (Y123 and Y125 in the

315 G.thermodenitrificans cytbd numbering). (Supplementary table 6). This suggests that the OR-C

316 and OR-N families diverged from either of these two families and evolved after the qOR

317 reductases. The evolutionary analysis within this family is complicated by the high number of

318 independent gene duplication events. It appears that qOR4b, OR-N5b, OR-N3b, OR-N4b and

319 OR-C1b subfamilies were the result of gene duplication events (Figure 1). In fact, OR-3a and

320 OR-3b cydA share 50 % sequence similarity. Additionally, the presence of OR-N1-type and OR-

321 N2-type cydA in the same operon in some Bacteria and the extent of similarity between them (up

Murali et al. ISMEJ-21-00087A 14

322 to 40%) suggest that they were part of yet another gene duplication. The importance of gene

323 duplication in protein evolution and functional diversification is well-known54. The nature this

324 process has taken in the cytochrome bd-type oxygen reductases is interesting - a majority of the

325 cydA paralogs have maintained the architecture associated with oxygen reduction and all of them

326 have maintained the His19 ligand to the active site heme d (as per the E. coli structure).

327 Additionally, all the above-mentioned duplication events appear to have resulted in a complex of

328 multiple cydA-like proteins with the possible exception of OR-N1 and OR-N2. OR-N2 is often

329 found in operons without another cydA-like protein (Figure 1). His19 and heme d is found near

330 the interface of subunit I and subunit II in the cydAB structures and the complete conservation of

331 these features with a change in their interacting partner, is suggestive of the process of

332 duplication and interface evolution recently investigated in hemoglobin55. Future work in the

333 biochemical and structural characterization of the various cytbd families will help us develop

334 insight into the driving forces behind the evolution of this superfamily. Presently, it is clear that

335 the defining characteristic of the cytbd superfamily is the di-heme oxygen reduction site found in

336 the first four helices of cydA homologs. Our analysis suggests that the bd protein scaffold was

337 diversified multiple times to perform O2 chemistry in unique environments, possibly to function

338 with different electron donors.

339 Conclusions

340 The superfamily of cytochrome bd-type oxygen reductases is one of only two oxygen reductase

341 superfamilies that are widely distributed in Bacteria and Archaea. In the current work we have

342 demonstrated the large diversity of this superfamily using phylogenomics. In addition, we

343 biochemically characterized the CydAA’ from C. maquilingensis showing that cydAA’ is a

344 robust oxygen reductase. The isolated CydAA’ contained only b hemes and no heme d. Hence,

Murali et al. ISMEJ-21-00087A 15

345 C. maquilingensis CydAA’ is a bb’-type oxygen reductase and is the first such enzyme to be

346 purified and demonstrated to be a functional oxygen reductase. Finally, we demonstrate that

347 significant diversification of the cydA has occurred with the conserved oxygen reduction site

348 being adapted to multiple functions within various ecological niches.

349 Materials and Methods

350 Phylogenomic analysis of cytochrome bd sequences in the GTDB database

351 In order to reconcile the protein phylogeny of cytochrome bd oxygen reductases with species

352 taxonomy, we identified and mapped all cytbd to their respective species within the GTDB

353 database release8937. All cydA sequences were extracted from GTDB genomes using BLAST56 with an

354 e-value of 1e-1. The sequences were then aligned using muscle57 using the optional maxiters cut-off of 2.

355 The alignment was visualized on Jalview58 and sequences were filtered to remove cydA sequences

356 without characteristics of the quinol binding site or the proton channel. This filtration step was used to

357 remove subunits II but also resulted in the loss of a few subunits I within qOR1 that appear to have lost

358 the proton channel. The filtered set of cydA sequences were then classified using a Hidden Markov

359 Model (HMM)-based classifier trained to identify the families – qOR1, qOR2, qOR3, qOR4a, OR-C and

360 OR-N. The HMMs for those subfamilies and families are available in the supplementary material. The

361 presence or absence of cytbd in each species was tabulated and is available as Supplementary Table 2.

362 The all archaea species tree used to analyze the distribution of cytochrome bd oxygen reductases in

363 archaea was generated using Anvi’o41. A multiple sequence alignment was created by extracting all

364 ribosomal proteins from archaeal genomes using the HMM source Archaea_76. This alignment was then

365 used to generate a phylogenetic tree using FastTree as per Anvi’o’s default settings. This tree was

366 annotated using the data available in Supplementary Table 4 on the iTOL server59.

Murali et al. ISMEJ-21-00087A 16

367 The protein phylogeny of cytbd sequences was inferred using sequences of cytbd subunit I, cydA. These

368 were extracted from a taxonomically diverse set of genomes and metagenomes from IMG60, filtered with

369 UCLUST61 using a percentage identity cut-off of 0.6 and aligned using MUSCLE. The multiple sequence

370 alignment was used to infer a phylogenetic tree using RAxML62 on the CIPRES Science Gateway63 with

371 the PROTGAMMA substitution model, DAYHOFF matrix specification and a bootstrap analysis with

372 100 iterations.

373 Preparation of construct for of cytochrome bd oxidase from Escherichia coli

374 The genes encoding the bb’ oxygen reductase (Gene Object ID: 641276193-4) from C.

375 maquilengensis were PCR amplified using primers purchased from Integrated DNA Technology.

376 The genes were cloned into pET22b (Invitrogen) using 5’ NdeI and 3’ XhoI cut sites. The

377 inherent 6-Histidine tag in the vector was used to purify the protein. The vector was engineered

378 to use EGFP, GST or FLAG tags alternatively. The tag was added to subunit II in case of EGFP

379 and FLAG; a tag on both subunit I and II was attempted for the His-tag and GST tag. The

380 expression vector, along with pRARE (Novagen) was then transformed into (CBO

381 ΔcydBΔappC::kan) for protein expression.

382 Cell Growth and Protein Purification

383 A single colony was inoculated into 5 ml of LB (yeast extract and tryptone were

384 purchased from Acumedia and NaCl from Sigma-Aldrich) with 100 µg/ml Ampicillin and

385 incubated with shaking at 37 ŀ. The following day, the 5 ml culture was inoculated in 300 ml

386 LB with 100 µg/ml Ampicillin and grown overnight at 37 ŀ. On the third day, 10 ml of the

387 secondary culture was inoculated into twenty four of 2L flasks containing 1 L LB with 100

388 µg/ml Ampicillin, each. The flasks were incubated at 37 ŀ while shaking at 200 rpm, until the

Murali et al. ISMEJ-21-00087A 17

389 OD600 of the culture reached 0.6. The temperature was then lowered to 30 ŀ, and the culture

390 was incubated for 8 hrs or overnight.

391 The fully-grown cultures were then pelleted by spinning down at 8000 rpm for 8 minutes,

392 in 500 ml centrifuge bottles. The harvested cells were then resuspended in 100 mM Tris-HCl, 10

393 mM MgS04, pH 8 with DNaseI and a protease inhibitor cocktail from Sigma. The cells were

394 then homogenized using a Bamix Homogenizer, and passed through a Microfluidizer cell at 100

395 psi, three times, to lyse the cells. The soluble fraction of the lysate was then separated from the

396 insoluble by spinning down the lysate at 8000 rpm. Membranes were extracted from the soluble

397 fraction by centrifuging the soluble fraction at 42000 rpm for 4 hours.

398 Membranes were resuspended in 20 mM Tris, 300 mM NaCl, pH 8 and then solubilized

399 with 1% DDM or 1% SML. The solubilized membranes were spun down at 42000 rpm for 45

400 minutes to remove unsolubilized membranes. The supernatant was stirred with Ni-NTA resin for

401 1 hr and then loaded onto a column. The flow through was shown to contain the cydAA’ because

402 of its poor affinity for the nickel column. The flow through was then diluted in buffer to contain

403 50 mM salt and then loaded onto a DEAE column equilibriated with 20 mM Tris, pH 8, 0.05%

404 DDM. An elution gradient was run between 0-500 mM NaCl and cydAA’ was partially purified

405 from the fraction with higher absorbance at A412nm, corresponding to the soret peak for heme b

406 and used for assays and spectroscopy. This is similar to the first step for purification of

407 Escherichia coli.

408 UV-visible spectroscopy

409 Spectra of the protein were obtained using an Agilent DW-2000 Spectrophotometer in the

410 UV-visible region. The cuvette used has a pathlength of 1cm. The oxidized spectrum was taken

Murali et al. ISMEJ-21-00087A 18

411 of the air-oxidized protein. The enzyme was reduced with dithionite to obtain a reduced

412 spectrum.

413 Collection of Pyridine Hemochrome spectra and Heme Analysis

414 For the wildtype or mutants enzymes, 35 μl of the enzyme solution was mixed with an

415 equal volume of 40% pyridine with 200 mM NaOH. The oxidized spectra was measured in the

416 presence of ferricyanide and the reduced in the presence of dithionite. The values of heme b were

417 calculated according to the matrix suggested in46. The concentration of heme d was estimated

-1 -1 418 using the extinction coefficient ε(629-670nm) = 25 mM cm .

419 Measurement of oxygen reductase activity

420 Oxygen reductase activity was measured using the Mitocell Miniature Respirometer

421 MT200A (Harvard Apparatus). 5 mM DTT and 350 µM Q1 were used as electron donors to

422 measure oxygen reduction by C.maquilingensis cydAA’ and E.coli cytochrome bd. 150-250 µM

423 KCN was used to test the cyanide sensitivity of the enzymes.

424 Structural modelling of cydAA’ from Caldivirga maquilingensis

425 Sequences of subunit I from Geobacillus thermodenitrificans and Caldivirga

426 maquilingensis were aligned using a larger alignment comprising many hundreds of bb’

427 sequences made with the software MUSCLE. This alignment was used as to create a model of

428 subunit I from Caldivirga using the Geobacillus subunit I as a template on the Swiss Model

429 server. A model of subunit II was also created using subunit I as a template. (The alignments are

430 provided as Supplementary Figures S4 and S5) The model was then visualized using VMD

431 1.9.2beta1.

Murali et al. ISMEJ-21-00087A 19

432

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585 List of Tables

586 Table 1. Expression of cydAA’ in the environment estimated using publicly available

587 metatranscriptomes. cydA homologs from the metatranscriptomic data available on the IMG website

588 were extracted using a BLASTP cutoff of 1e-5. The short fragments found in metatranscriptomic data

589 were matched with the full corresponding protein sequence based on the best hit in the NCBI database.

590 Table 2. Oxygen reduction activity of E. coli cydAB and C. maquilingensis cydAA’ in the presence

591 of 350 µM coenzyme Q1 and 5 mM DTT.

592 Supplementary Table 1. Total number of various cydA families and subfamilies in the GTDB. All

593 cydA sequences were extracted from GTDB genomes using BLAST with an e-value of 1e-1. The

594 sequences were then filtered to remove cydA sequences without characteristics of the quinol binding site

595 and then classified using a Hidden Markov Model (HMM)-based classifier trained to identify the families

596 – qOR1, qOR2, qOR3, qOR4a, OR-C, OR-N. The total number of cydA sequences in each of these

597 families and subfamilies were summed to generate this table.

598 Supplementary Table 2. Distribution of cydA subfamilies by genome in GTDB. All cydA sequences

599 were extracted from GTDB genomes using BLAST with an e-value of 1e-1. The sequences were then

600 filtered to remove cydA sequences without characteristics of the quinol binding site and then classified

601 using a Hidden Markov Model (HMM)-based classifier trained to identify the families – qOR1, qOR2,

602 qOR3, qOR4a, OR-C, OR-N. Labelled cydA sequences were then mapped back to each species to

603 generate this table.

604 Supplementary Table 3. Distribution of cydA subfamilies by phyla in GTDB. All cydA sequences

605 were extracted from GTDB genomes using BLAST with an e-value of 1e-1. The sequences were then

606 filtered to remove cydA sequences without characteristics of the quinol binding site and then classified

607 using a Hidden Markov Model (HMM)-based classifier trained to identify the families – qOR1, qOR2,

Murali et al. ISMEJ-21-00087A 26

608 qOR3, qOR4a, OR-C, OR-N. Labelled cydA sequences were then mapped back to each species and the

609 cydA sequences from each family/subfamily were summed across each phyla.

610 Supplementary Table 4. Distribution of quinol oxidizing cytbd in archaeal genomes found in the

611 GTDB. All cydA sequences were extracted from GTDB genomes using BLAST with an e-value of 1e-1.

612 The sequences were then filtered to remove cydA sequences without characteristics of the quinol binding

613 site and then classified using a Hidden Markov Model (HMM)-based classifier trained to identify the

614 families – qOR1, qOR2, qOR3, qOR4a. Labelled cydA sequences were then mapped back to each species

615 within the domain archaea to generate this table.

616 Supplementary Table 5. Growth conditions and temperature for organisms containing cydAA’.

617 Growth conditions, sensitivity to oxygen and temperature are detailed with references in this table to see

618 if there is a pattern to the conditions under which cydAA’ is typically found.

619 Supplementary Table 6. Conserved features residues identified in cytbd families without quinol

620 oxidizing features - qOR4b and subfamilies OR-C1a, OR-N1, OR-N2, OR-N3a, OR-N3b, OR-N4a,

621 OR-N4b, OR-N5a and OR-N5b. Conserved residues were identified using multiple sequence alignments

622 of cydA sequences from the above families. The presence or absence of the conserved residues for the

623 three hemes, proton channel, quinol binding site are marked.

624 Supplementary Table 7. Number of heme c binding sites in cytbd sequences from OR-C1a/OR-C1b

625 subfamilies. Number of heme c binding sites were counted using a python script that identifies the

626 number of CXXCH motifs in each protein sequence. The OR-C1a sequences from Desulfovibrionia

627 appear to have the greatest number of heme c binding sites – up to 8.

628

629

630

Murali et al. ISMEJ-21-00087A 27

631 List of multiple sequence alignments

632 Supplementary multiple sequences alignment MSA1. Multiple sequence alignment of sequences from

633 cydA subfamilies qOR1, qOR2, qOR3, qOR4a, qOR4b and families OR-C1a and OR-N. OR-N is not

634 split into subfamilies in this alignment. Various families and subfamilies are grouped when visualized in

635 Jalview and amino acids are colored using a ClustalX algorithim with a greater than 90 % identity. This

636 alignment was manually curated to improve the alignment and reduce the number of gaps.

637 Supplementary multiple sequences alignment MSA2. Multiple sequence alignment of sequences from

638 cydA subfamilies qOR1, qOR2, qOR3, qOR4a, qOR4b. OR-C1a, OR-N1, OR-N2. OR-N3a/3b, OR-

639 N4a/4b, OR-N5a and OR-N5b. Various families and subfamilies are grouped when visualized in Jalview

640 and amino acids are colored using a ClustalX algorithim with a greater than 90 % identity.

641 Supplementary multiple sequences alignment MSA3. Multiple sequence alignment of sequences from

642 all 15 cydA subfamilies qOR1, qOR2, qOR3, qOR4a, qOR4b. OR-C1a, OR-C1b OR-N1, OR-N2. OR-

643 N3a/3b, OR-N4a/4b, OR-N5a and OR-N5b.

644

645 List of Figures

646 Figure 1. Families within the cytochrome bd-type oxygen reductase superfamily. The cytochrome-bd

647 type oxygen reductase superfamily is divided into 3 families – qOR, OR-C and OR-N, primarily defined

648 by the presence of the quinol binding site in the first, the presence of heme c binding site in the second

649 and the abundance of OR-N enzymes in nitrospirota. The above schematic represents the various

650 subfamilies within each family, which are defined by the phylogenetic clustering shown in Supplementary

651 Figure 1). The operon context and putative complex arrangement of each cydA-containing enzyme is also

652 shown with a reference protein accession number and source microorganism. The potential gene

Murali et al. ISMEJ-21-00087A 28

653 duplication events are highlighted in yellow. A legend is also provided to mark the related conserved

654 domains in the same colors and redox co-factors such hemes and iron-sulfur clusters.

655 Figure 2. Phylogeny of quinol-oxidizing cytochrome bd-type oxygen reductases. Sequences of cytbd

656 subunit I, cydA were extracted from a taxonomically diverse set of genomes and metagenomes from

657 IMG, filtered with UCLUST using a percentage identity cut-off of 0.6 and aligned using MUSCLE. The

658 multiple sequence alignment was used to infer a phylogenetic tree using RAxML. The RAxML tree

659 topology was similar to that inferred by PhyML and Mr. Bayes. The cydA sequences which do not

660 contain the quinol binding site, from the OR-C and OR-N families as well as qOR4b, were used as the

661 outgroup. At least four monophyletic clades of typical cydA sequences that contain the O2- and quinol

662 binding site could be defined – qOR1, qOR2, qOR3 and qOR4a. The long branch within the qOR1 clade

663 comprises a number of cytbd which are highly similar to enzymes from this clade but are missing the

664 proton channel. Subunit I of cydAA’ is from the qOR4a-family.

665 Figure 3. Distribution of cytochrome bd-type oxygen reductases in Archaea. Concatenated gene

666 alignments were made from the archaea genomes in GTDB using Anvi’o. A phylogenetic tree was made

667 from the concatenated gene alignments using FastTree. All cydA sequences were extracted from GTDB

668 genomes using BLAST with an e-value of 1e-1. The sequences were then filtered to remove cydA

669 sequences without characteristics of the quinol binding site and then classified using a Hidden Markov

670 Model (HMM)-based classifier trained to identify the families – qOR1, qOR2, qOR3 and qOR4a. cydA

671 sequences from each family were then mapped back to each species, and visualized along with the species

672 tree on the iTOL server. Most phyla of the domain archaea were distinguished by color and a few classes

673 of the phylum Crenarchaeota were labelled to emphasize the presence of cydAA’. It is clear that cydAA’

674 is almost exclusive to the order Thermoproteales and Desulfurococcales.

675 Figure 4. Biochemical characteristics of cydAA’ from Caldivirga maquilingensis. (a and b.) UV-

676 visible spectra of cytochrome bd-type oxygen reductase purified from Escherichia coli and Caldivirga

677 maquilingensis, respectively. C. Pyridine hemochrome spectra of cydAA’ from Caldivirga

Murali et al. ISMEJ-21-00087A 29

678 maquilingensis revealing the absence of heme d in the partially purified enzyme. D. Oxygen reductase

679 activity of cydAA’ from C. maquilingensis shows that it is highly active and cyanide insensitive. It is

680 sensitive to Aurachin C1-10, a quinol binding site inhibitor which also inhibits E. coli cytochrome bd.

681 List of supplementary figures

682 Supplementary Figure 1. Phylogenetic clustering of all cydA-like sequences. cydA sequences were

683 extracted from a taxonomically diverse set of genomes and metagenomes from IMG and aligned using

684 MUSCLE. The multiple sequence alignment was used to infer a phylogenetic tree using RAxML. The

685 RAxML tree topology was similar to that inferred by PhyML. The three families, qOR, OR-C and OR-N

686 are clearly separated, and 15 subfamilies were designated based on the clustering observed and

687 identifiable sequence characteristics.

688 Supplementary Figure 2. Sequence characteristics of qOR4a-cydA. a. An unrooted phylogenetic tree

689 of cydA sequences from archaea including both qOR4a-type cydA and cydA of the qOR1, qOR2 and

690 qOR3 (in red) types was generated using RaxML. qOR4a type cydA have some internal clusters,

691 identified with a shaded box in green, blue and purple. Characteristics unique to the cluster, when

692 identifiable were indicated. For e.g., the presence of the insertion in the proton channel. b. A multiple

693 sequence alignment of the sequences present in the above clusters, the background of each sequence

694 cluster shaded in red, green, blue and purple according to the colors in the tree in a. Conserved residues

695 corresponding to the ligands, proton channel and a few residues expected to participate in proton-coupled

696 electron transfer are marked. Significantly, several qOR4a-type cydA have a lysine substituted for M393

697 (E. coli numbering) in the active site suggesting an alteration of the midpoint potential of heme b558 in

698 those enzymes.

699 Supplementary Figure 3. GFP-tagged cydAA’ from Caldivirga maquilingensis. The presence of

700 cydAA’ during protein purification protocol was verified by looking at elution fractions under UV-light.

701 Three glass vials containing (from leftmost) elution buffer, an elution fraction containing GFP-tagged

Murali et al. ISMEJ-21-00087A 30

702 cydAA’ and a fraction without cydAA’ are compared. The green fluorescence in the cydAA’ containing

703 fraction is easily distinguishable.

704 Supplementary Figure 4. Mass spectrometric identification of subunit I of cydAA’ from Caldivirga

705 maquilingensis. Partially purified cydAA’ was digested with Chymotrypsin and the digested peptides

706 were separated by HPLC and infused into a Thermo LTQ Velos ETD Pro Mass Spectrometer. The mass

707 fragments recovered after MS/MS fragmentation were subject to analysis by Mascot Distiller and Mascot

708 version 2.4. The analysis revealed peptides from subunit I of cydAA’ in the protein preparation with a

709 MASCOT score of 85.

710 Supplementary Figure 5. SDS-PAGE gel electrophoresis of partially purified cydAA’. A. Cell lysate

711 was loaded onto a Ni-NTA column (Lane 1). The flow-through was loaded onto a Q-sepharose column

712 and subject to elution by changing the salt concentration from 0-500 mM NaCl. Three elution peaks

713 (Lanes 2,3,4) which absorbed at 412 nm were pooled, concentrated and diluted to 50 mM NaCl and then

714 loaded onto a DEAE-Sepharose column and subject to elution under a salt gradient from 0-500 mM NaCl.

715 The elution fraction (Lane 6) which absorbed at 412 nm was pooled and concentrated and used to identify

716 electrophoresis patterns. Assays and spectra were obtained with a sample that was subject to a simpler

717 purification protocol – Ni-NTA followed by DEAE-sepharose because the yield was poor from the 3-step

718 purification protocol. Lane 5 was the Precision Plus Dual Color Standard (Bio-Rad). Subunits I and II are

719 similar in size to the subunits from E.coli cytbd (B). B. Electrophoresis patterns of purified E.coli cytbo3

720 and cytbd.

721 Supplementary Figure 6. Sequence characteristics of qOR4b-cydA from Caldivirga maquilingensis

722 (also referred to as cydA’). a. A topological representation of cydA’ using HMMTOP. The amino acids

723 conserved above 90% identity are shaded in black. b. A multiple sequence alignment of sequences from

724 qOR4a-cydA and qOR4b-cydA family. The former sequences are highlighted with the purple background

725 while the latter are highlighted with a gray background. The absence of the proton channel residues E99

726 and E109 is apparent. The ligand to heme d, His19 and the proton channel residue H126 are completely

Murali et al. ISMEJ-21-00087A 31

727 conserved. The ligands to heme b558 (H186 and M393) and other amino acids typically associated with the

728 quinol binding site in helices V-VIII are not well conserved. Two threonines Thr71 and Thr74 in

729 C.maquilingensis which take the place of Leu71 and Glu74 are completely conserved.

730 Supplementary Figure 7. Structural model of subunits I from Geobacillus thermodenitrificans

731 and Caldivirga maquilingensis respectively. The homology model of cydA from Caldivirga

732 maquilingensis was generated using the Swiss PDB viewer and visualized using VMD. The boxed

733 regions reveal more polar residues in Geobacillus, represented by red and blue, while aromatic

734 residues are colored in green.

Murali et al. ISMEJ-21-00087A 32 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.16.426971; this version posted January 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Figure 1. Diversity of the cytochrome bd oxygen reductase superfamily. The cytochrome bd oxygen reductase superfamily is divided into 3 families based on phylogenetics and structure – qOR, OR-C and OR-N. qOR is defined by the presence of the quinol binding site in subunit I (cydA). OR-C is missing the quinol binding site but has a heme c binding site in subunit I. OR-N is also missing the quinol binding site and is commonly found in operons containing alternative electron donors. Various subfamilies within each family are also shown (Supplementary Figure 1). The operon context and putative protein complex arrangement of each cydA-containing enzyme is also shown with a reference protein accession number and source microorganism. The potential gene duplication events are highlighted in yellow. A legend is also provided to mark the related conserved domains in the same colors and redox co-factors such hemes and iron-sulfur clusters. A more detailed explanation of the figure including a description of the various subunits and characteristics of the families and subfamilies is provided in Supplementary Material.

Figure 2. Phylogeny of quinol-oxidizing cytochrome bd-type oxygen reductases. At least four clades of quinol-oxidizing cytochrome bd-type oxygen reductases could be identified – qOR1, qOR2, qOR-3 and qOR-4a. The long branch within the qOR1 clade (red star) is comprised of sequences missing the proton channel that is conserved in all other quinol-oxidizing cytochrome bd-type oxygen reductases. Subunit I of cydAA’ is from the qOR4a family. The cytochrome bd- type oxygen reductases that do not contain the quinol binding site (OR-C, OR-N, and qOR-4b families) were used as the outgroup.

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la r c la 8 9 1 5 7 3 9 0 8 2 8 b 3 8

s T T h s % % M G 8 5 5 8 7 9 5 - O s 5 3 s T h h a s 8 I 9 5 7 8 M p a a a e a 6 3 G Ib 9 5 5 % 3 0 T r h l u r % I - 5 G s 0

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0 1 h p a u c rc e 1 p M - M 5 0 4 I b O 0 9

a 0 e m h h u 4 0 G O II M G s 2 9 - 3 0 5

4 e 0 u a a m 7 0 I G 5 b I G p 4 8 O 2

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% M m 5 s t m m p 5 9 O - p 5 Ib O - 2 7 5 s 0 23

7 p a 0 8 5 O 0 s - O 7 2 p 0 s

3 . G s 6 0 e s s 0 2 5 0 p O 5 5 3 5 0 2 75

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Ib 2 0 0 7 5 p s 5 0 p s 0 2 1

0 9 - G 0 5 4 0 0 2 0 p 0 2 s 0 M p 9 7 2 r . 5 O I 2 9 2 7 0 0 2 p 0 G 0 1 5 % 9 3 I b 5 5 5 2 2 2 0 0 49 0 2 0 5 9 7

. - 0 7 0 50 7 4 2 9 9 0 5 IIb 2 6 5

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% 0 2 0 8 1 2 9 8 1

9 G 0 s 5 85 5 6 8 5 9 2 5 6 M

5 I 2 p 5 5 0 3 5 s 0 G

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7 0 5 1

5 4 a 5 5 p o Cyt bd rm e families Th qOR4a qOR3 qOR1 qOR2 Figure 3. Distribution of cytochrome bd-type oxygen reductases in Archaea. Cytochrome bd-type oxygen reductases are sporatically distributed throughout the Archaea. The qOR4a family (cydAA’) is predominantly found within the Thermoproteales and Desulfurococcales orders of Crenarchaeota. bioRxiv preprint doi: https://doi.org/10.1101/2021.01.16.426971; this version posted January 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Figure 4. Biochemical characteristics of cytochrome bb’ (cytbb’) from Caldivirga maquilingensis. (A and B.) UV-visible spectra of cytochrome bd-type oxygen reductases purified from Escherichia coli and Caldivirga maquilingensis, respectively. C. Pyridine hemochrome spectra of Caldivirga maquilingensis cytbb’ reveals the absence of heme d in the partially purified enzyme. D. Oxygen reductase activity of cytbb’ from C. maquilingensis shows that it is highly active and cyanide insensitive. It is sensitive to Aurachin C1-10, a quinol binding site inhibitor which also inhibits E. coli cytochrome bd.

Table 1. cydAA’ is expressed in many environments. Protein expression is estimated based on read counts in metatranscriptomes. Genome_ID Genome_Name Locus_Tag Reads Best BLAST Hit NCBI Organism Ga0040881_1063211 246 ESQ23817.1 Acidilobus sp. OSP8 Ga0040881_1110491, 106 AMD31390.1 Acidilobus sp. 7A Ga0099831_11874701 42 Ferric microbial mat communities from Yellowstone Ga0040881_1111231 27 WP_081246098.1 Thermoproteus sp. CP80 National Park, Wyoming, USA - One Hundred 3300003719 Ga0040881_1134581 25 WP_066793619.1 Caldivirga sp. MU80 Spring Plain (OSP_B) (Metagenome Metatranscriptome) (*) (MER-FS) (assembled) Ga0040881_1142191, 2174 NAY81522.1 Thaumarchaeota archaeon Ga0040881_1205091 12 Ga0040881_1202971 5 KUO89797.1 Caldivirga sp. CIS_19 Ga0040881_1228021, 8 KUO80886.1 Vulcanisaeta sp. JCHS 4 Ga0040873_1002501 4784 AMD31390.1 Acidilobus sp. 7A Hypersaline microbial mat communities from Ga0040873_1003761 1921 EQB65596.1 Thermoplasmatales Yellowstone National Park, Wyoming, USA - 3300003723 Ga0040873_1011521 2174 KUO93148.1 Thermocladium sp. ECH_B Beowulf (BE_B) (Metagenome Metatranscriptome) Ga0040873_1013971 707 PMP91269.1 Caldisphaera sp. (*) (MER-FS) (assembled) Ga0040873_1028371 244 NAY81522.1 Thaumarchaeota archaeon Hypersaline microbial mat communities from Ga0040875_1014081 163 AMD31390.1 Acidilobus sp. 7A Yellowstone National Park, Wyoming, USA - 3300003709 Grendel (GRN_C) (Metagenome Ga0040875_1034841 11 KUO93148.1 Thermocladium sp. ECH_B Metatranscriptome) (*) (MER-FS) (assembled)

Ga0099835_1035811 192 NAY81522.1 Thaumarchaeota archaeon Iron oxide microbial mat communities from Ga0099835_1427011, 4 KUO93148.1 Thermocladium sp. ECH_B Yellowstone National Park, Wyoming, USA - 3300007166 Ga0099835_1431661 3 BED_top_diel_T=1 metaT (Metagenome Ga0099835_1456681 2 PMP93815.1 Nitrosphaera sp. Metatranscriptome) (*) (MER-FS) (assembled) Ga0099835_1510461 17 KUO89797.1 Caldivirga sp. CIS_19

Iron oxide microbial mat communities from Ga0099836_1305913 60 NAY81522.1 Thaumarchaeota archaeon Yellowstone National Park, Wyoming, USA - Ga0099836_1428691 2 WP_066793619.1 Caldivirga sp. MU80 3300007164 BED_top_diel_T=3 metaT (Metagenome Ga0099836_1428931, 3 KUO93148.1 Thermocladium sp. ECH_B Metatranscriptome) (*) (MER-FS) (assembled) Ga0099836_1472421 3 Iron oxide microbial mat communities from Ga0099838_1606901 3 KUO93148.1 Thermocladium sp. ECH_B Yellowstone National Park, Wyoming, USA - 3300007168 BED_top_diel_T=7 metaT (Metagenome Ga0099838_1754862 40 NAY81522.1 Thaumarchaeota archaeon Metatranscriptome) (*) (MER-FS) (assembled)

Iron oxide microbial mat communities from Ga0099839_1320821 2 NAZ28310.1 Caldivirga sp. Yellowstone National Park, Wyoming, USA - 3300007161 Ga0099839_1444841, 19 NAY81522.1 Thaumarchaeota archaeon BED_top_diel_T=8 metaT (Metagenome Ga0099839_1444842, 4 Metatranscriptome) (*) (MER-FS) (assembled) Ga0099839_1513781 Ga0099840_1194611, 6 KUO93148.1 Thermocladium sp. ECH_B Iron oxide microbial mat communities from Ga0099840_1228901 Yellowstone National Park, Wyoming, USA - Ga0099840_1208591, 29 NAY81522.1 Thaumarchaeota archaeon 3300007574 ECH_B_top_diel_T=1 metaT (Metagenome Ga0099840_1293341 27 Metatranscriptome) (*) (MER-FS) (assembled) Ga0099840_1307751, 7 Ga0099840_1212061 16 AMD31390.1 Acidilobus sp. 7A Ga0099841_1138611 5 WP_117355195.1 Acidilobus sp. 7A Iron oxide microbial mat communities from Ga0099841_1140711, 23 NAY81522.1 Thaumarchaeota archaeon Yellowstone National Park, Wyoming, USA - 3300007486 Ga0099841_1141101 12 ECH_B_top_diel_T=5 metaT (Metagenome Ga0099841_1256151 7 NAZ28310.1 Caldivirga sp. Metatranscriptome) (*) (MER-FS) (assembled) Ga0099841_1293981 15 KUO93148.1 Thermocladium sp. ECH_B Iron oxide microbial mat communities from Ga0099844_1215141, 10 NAY81522.1 Thaumarchaeota archaeon Yellowstone National Park, Wyoming, USA - Ga0099844_1308701 10 3300007575 ECH_C_top_diel_T=7 metaT (Metagenome Metatranscriptome) (*) (MER-FS) (assembled) Metatranscriptome of extremophilic microbial mat Ga0187838_10229991 154 WP_014289867.1 Pyrobaculum ferrireducens communities from Yellowstone National Park, 3300021851 Wyoming, USA - CONBC_RNA (Metagenome Ga0187838_11515921 155 KUK06933.1 Archaeoglobus fulgidus Metatranscriptome) (*) (MER-FS) (assembled) Ga0401895_061319_2_36 HGD34321.1 Candidatus Korarchaetoa Metatranscriptome of soil microbial communities 1 archaeon from Old Woman Creek estuary, Ohio, United 3300037625 - States - Aug_M1_C1_D5_B (Metagenome Metatranscriptome) (*) (MER-FS) (assembled)

Metatranscriptome of tropical peat soil microbial Ga0187794_17837561 5 PMP74969.1 Aciduliprofundum sp. communities from peatlands in Department of 3300019273 Meta, Colombia - 0116_SJ02_MP02_20_MT (Metagenome Metatranscriptome) (*) (MER-FS) (assembled) Metatranscriptome of tropical peat soil microbial Ga0187796_12966161 31 HHN53578.1 Nitrosphaera archaeon communities from peatlands in Department of 3300019264 Meta, Colombia - 0116_SJ02_MP15_20_MT (Metagenome Metatranscriptome) (*) (MER-FS) Ga0187796_15754521 8 PMP74969.1 Aciduliprofundum sp. (assembled) Metatranscriptome of tropical peat soil microbial Ga0187799_12787231 6 HHN53578.1 Nitrosphaera archaeon communities from peatlands in Department of 3300019211 Meta, Colombia - 0216_BV02_MP12_10_MT (Metagenome Metatranscriptome) (*) (MER-FS) (assembled) Metatranscriptome of tropical peat soil microbial Ga0187800_11075051 3 PMP74969.1 Aciduliprofundum sp. communities from peatlands in Department of 3300019278 Meta, Colombia - 0216_BV02_MP12_20_MT (Metagenome Metatranscriptome) (*) (MER-FS) (assembled) Thermal spring microbial communities from Beowulf Ga0040879_1097101 63 NAY81522.1 Thaumarchaeota archaeon Spring, Yellowstone National Park, Wyoming, USA - 3300003730 Beowulf (BE_D) (Metagenome Metatranscriptome) Ga0040879_1273451 7 NAZ28310.1 Caldivirga sp. (*) (MER-FS) (assembled) bioRxiv preprint doi: https://doi.org/10.1101/2021.01.16.426971; this version posted January 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.

Table 2. Oxygen reduction activity of E. coli cytbd and C. maquilingensis cytbb’ in the presence of 350 µM coenzyme Q1 and 5 mM DTT.

Oxygen reduction activity Protein (e-/s)

Caldivirga maquilingensis cytbb’ 333 Ə 20 (cydAA’)

Escherichia coli cytbd (cydAB) 1065 Ə 73