Editing Last universal common ancestor (section)

=== Undersampled protein families ===

Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing [[Convergent evolution|convergence]] or horizontal gene transfer events to vertical descent; on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events. A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K<sup>+</sup>-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K<sup>+</sup>/Na<sup>+</sup> ratio, {{chem|NH|4|+}}, Fe<sup>2+</sup>, CO<sup>2+</sup>, Ni<sup>2+</sup>, Mg<sup>2+</sup>, Mn<sup>2+</sup>, Zn<sup>2+</sup>, pyrophosphate, and {{chem|PO|3-|4}} which would imply a terrestrial [[hot spring]] habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to [[Autotroph|autotrophy]] (the ability of an organism to create its own [[organic matter]]), suggesting that the LUCA had a [[Heterotroph]]ic lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.<ref>{{Cite journal |last1=Mulkidjanian |first1=Armen Y. |last2=Bychkov |first2=Andrew Yu |last3=Dibrova |first3=Daria V. |last4=Galperin |first4=Michael Y. |last5=Koonin |first5=Eugene V. |author5-link=Eugene V. Koonin |year=2012 |title=Origin of first cells at terrestrial, anoxic geothermal fields |journal=[[Proceedings of the National Academy of Sciences of the United States of America|Proceedings of the National Academy of Sciences]] |volume=109 |issue=14 |pages=E821-30 |bibcode=2012PNAS..109E.821M |doi=10.1073/pnas.1117774109 |pmc=3325685 |pmid=22331915 |doi-access=free}}</ref> <!--[[Nick Lane]] argues that Na<sup>+</sup>/H<sup>+</sup> antiporters could readily explain the low concentration of Na<sup>+</sup> in the LUCA and its descendants.-->

The presence of the energy-handling enzymes [[CODH]]/[[Acetyl-CoA|acetyl-coenzyme A]] synthase in LUCA could be compatible not only with being an [[autotroph]] but also with life as a [[mixotroph]] or [[heterotroph]].<ref>{{cite journal |last1=Adam |first1=Panagiotis S. |last2=Borrel |first2=Guillaume |last3=Gribaldo |first3=Simonetta |date=6 February 2018 |title=Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes |journal=PNAS |volume=115 |issue=6 |pages=E1166–E1173 |bibcode=2018PNAS..115E1166A |doi=10.1073/pnas.1716667115 |pmc=5819426 |pmid=29358391 |doi-access=free}}</ref> Weiss et al. in 2018 replied that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.<ref name="Weiss Preiner Xavier 2018"/>

A 2024 study directly estimated the order in which amino acids were added into the genetic code from early protein sequences. It found that amino acids that bind metals, and those that contain sulphur, came early in the sequence. The study suggests that sulphur metabolism and catalysis involving metals were important elements of life at the time of LUCA.<ref name="Wehbi Wheeler Morel 2024">{{cite journal |last1=Wehbi |first1=Sawsan |last2=Wheeler |first2=Andrew |last3=Morel |first3=Benoit |last4=Manepalli |first4=Nandini |last5=Minh |first5=Bui Quang |last6=Lauretta |first6=Dante S. |last7=Masel |first7=Joanna |author7link=Joanna Masel |title=Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains |journal=Proceedings of the National Academy of Sciences |volume=121 |issue=52 |date=24 December 2024 |pages=e2410311121 |pmid=39665745 |pmc=11670089 |doi=10.1073/pnas.2410311121 |doi-access=free }}</ref>