On 2017 Feb 04, James Hemp commented:

Ducluzeau et al. erroneously cited our paper 'Adaptation of aerobic respiration to low O2 environments.; PMID: 21844375' multiple times as making claims that aerobic respiration existed in LUCA.

"Aerobic respiration is thus proposed to have been operating in the last universal common ancestor (LUCA) of cellular life in one scenario [1,12,13], whereas others favour the later emergence of O2 respiration from within an anaerobic type of respiration such as the denitrifying pathway [7,11]." - Our paper never mentioned LUCA, nor the presence of aerobic respiration or heme-copper oxygen reductases in LUCA.

"These lines of reasoning lead Brochier-Armanet et al. to propose SoxM (A), the enzyme most widely distributed in extant organisms, as the most ancestral O2R present already in the LUCA, whereas all other groups of O2Rs and NORs would be later evolutionary emanations from this ancestral SoxM (A)-type enzyme. This scenario was subsequently adopted by the Gennis group and is hence used by these colleagues as a basis for interpreting structural and functional results [1]." - We definitely did not adopt the proposal by Brochier-Armanet et al. to interpret our results, nor did we cite their work in the paper. The phylogenetic framework used to interpret our results was from our work "Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling.; PMID: 18183358". In it we state "Phylogenetic analyses strongly suggest that the heme–copper oxygen reductases originated within the Bacteria and members were later transferred to the Archaea.", and show a phylogenetic tree of the B-family and relatives evolving from the A-family.

"Consequently, Han et al. [1] consider that LUCA invented the low-affinity SoxM (A) enzyme in a high O2 environment, and the high-affinity SoxB (B)- and cbb3 (C)-type O2Rs would have appeared only when life started to colonize microaerobic habitats. This scenario therefore predicts a LUCA thriving at O2 levels of higher than 1 μM. To the best of our knowledge, no geochemical evidence for such high concentrations of O2 prior to the GOE has been reported so far." - We never said that any oxygen reductases were present in LUCA or before the GOE.

On 2017 Feb 04, James Hemp commented:

Ducluzeau et al. erroneously cited our paper 'Adaptation of aerobic respiration to low O2 environments.; PMID: 21844375' multiple times as making claims that aerobic respiration existed in LUCA.

"Aerobic respiration is thus proposed to have been operating in the last universal common ancestor (LUCA) of cellular life in one scenario [1,12,13], whereas others favour the later emergence of O2 respiration from within an anaerobic type of respiration such as the denitrifying pathway [7,11]." - Our paper never mentioned LUCA, nor the presence of aerobic respiration or heme-copper oxygen reductases in LUCA.

"These lines of reasoning lead Brochier-Armanet et al. to propose SoxM (A), the enzyme most widely distributed in extant organisms, as the most ancestral O2R present already in the LUCA, whereas all other groups of O2Rs and NORs would be later evolutionary emanations from this ancestral SoxM (A)-type enzyme. This scenario was subsequently adopted by the Gennis group and is hence used by these colleagues as a basis for interpreting structural and functional results [1]." - We definitely did not adopt the proposal by Brochier-Armanet et al. to interpret our results, nor did we cite their work in the paper. The phylogenetic framework used to interpret our results was from our work "Diversity of the heme-copper superfamily in archaea: insights from genomics and structural modeling.; PMID: 18183358". In it we state "Phylogenetic analyses strongly suggest that the heme–copper oxygen reductases originated within the Bacteria and members were later transferred to the Archaea.", and show a phylogenetic tree of the B-family and relatives evolving from the A-family.

"Consequently, Han et al. [1] consider that LUCA invented the low-affinity SoxM (A) enzyme in a high O2 environment, and the high-affinity SoxB (B)- and cbb3 (C)-type O2Rs would have appeared only when life started to colonize microaerobic habitats. This scenario therefore predicts a LUCA thriving at O2 levels of higher than 1 μM. To the best of our knowledge, no geochemical evidence for such high concentrations of O2 prior to the GOE has been reported so far." - We never said that any oxygen reductases were present in LUCA or before the GOE.