User:PerenniallyLoamy/Hopanoids

Lead
Calvin, this is a great start and really good content. I think it would benefit from more detailed heading/subheading/sub-subheading breakdown, so that you don't just have 8 straight paragraphs of text about 2-methyl hopanoids, for example. Its an encyclopedia article not a review paper... Also think about what graphics will best support this story. A few more specific comments: - “oldest detected triterpenoid fossils” should probably say something like “that are unambiguously authentic” or maybe just "undisputed", since there are (apparently) older ones that have been detected but are disputed as likely contaminants. - paragraph about antiquity of synthesis would maybe be better in the biosynthesis section? (I don’t feel strongly about this, and do see why it is also relevant to paleobiology) - “later rejected altogether” should probably say something like “later rejected due to concerns about modern contamination”

In paleobiology
Hopanoids have been estimated to be the most abundant natural products on Earth, remaining in the organic fraction of all sediments, independent of age, origin or nature. Biomolecules like DNA and proteins are degraded during diagenesis, but polycyclic lipids persist in the environment over geologic timescales due to their fused, stable structures. Although hopanoids and sterols are reduced to hopanes and steranes during deposition, these diagenetic products can still be useful biomarkers, or molecular fossils, for studying the coevolution of early life and Earth.

Currently, the oldest detected undisputed triterpenoid fossils are Mesoproterozoic okenanes, steranes, and methylhopanes from a 1.64 Gya basin in Australia. However, molecular clock analyses estimate that the earliest sterols were likely produced around 2.3 Gya, around the same time as the Great Oxidation Event, with hopanoid synthesis arising even earlier.

For several reasons, hopanoids and squalene-hopene cyclases have been hypothesized to be more ancient than sterols and oxidosqualene cyclases. First, diplopterol is synthesized when water quenches the C-22 carbocation formed during polycyclization. This indicates that hopanoids can be made without molecular oxygen and could have served as a sterol surrogate before the atmosphere accumulated oxygen, which reacts with squalene in a reaction catalyzed by squalene monooxygenase during sterol biosynthesis. Furthermore, squalene binds to squalene-hopene cyclases in a low-energy, all-chair conformation while oxidosqualene is cyclized in a more strained, chair-boat-chair-boat conformation. Squalene-hopene cyclases also display more substrate promiscuity in that they cyclize oxidosqualene in vitro, causing some scientists to hypothesize that they are evolutionary predecessors to oxidosqualene cyclases. Other scientists have proposed that squalene-hopene and oxidosqualene cyclases diverged from a common ancestor, a putative bacterial cyclase that would have made a tricyclic malabaricanoid or tetracyclic dammaranoid product.

Proposal
2-methylhopanes, often quantified as the 2-α-methylhopane index, were first proposed as a biomarker for oxygenic photosynthesis by Roger Summons and colleagues following the discovery of the precursor lipids, 2-methylhopanols, in cyanobacterial cultures and mats. The subsequent discovery of 2-α-methylhopanes in 2.7 Ga shales from the Pilbara Craton of Western Australia suggested a 400 Ma gap between the evolution of oxygenic metabolism and the Great Oxidation Event, but these findings were later rejected due to potential contamination by modern hydrocarbons. Putative cyanobacterial presence on the basis of abundant 2-methylhopanes was also used to explain black shale deposition during Aptian and Cenomanian–Turonian Ocean Anoxic Events (OAEs) and the associated 15N isotopic signatures indicative of N2-fixation. In contrast, 2-α-methylhopane index values are relatively low across Frasnian and Famennian sediments corresponding to the Kellwasser event(s), though higher levels have been reported in later Lower Famennian sections.

Dispute
The status of 2-methylhopanoids as a cyanobacterial biomarker was challenged by a number of microbiological discoveries. Geobacter sulfurreducens was demonstrated to synthesize diverse hopanols, although not 2-methylhopanols, when grown under strictly anaerobic conditions. Furthermore, the anoxygenic phototroph Rhodopseudomonas palustris was found to produce 2-methylhopanols when grown anaerobically. This latter discovery also lead to the identification of the gene encoding the key methyltransferase hpnP. HpnP was subsequently identified in an acidobacterium and numerous alphaproteobacteria, and phylogenetic analysis of the gene concluded that it originated in the alphaproteobacteria and was acquired by the cyanobacteria and acidobacteria via horizontal gene transfer.

Among cyanobacteria, hopanoid production is generally limited to terrestrial cyanobacteria. Among marine cyanobacteria, culture experiments in conducted by Helen Talbot and colleagues concluded that only two marine species–Trichodesmium and Crocosphaera–produced bacteriohopanepolyols.

A later gene-based search for hpnP in available cyanobacterial genomes and Metagenome Assembled Genomes (MAGs) drew similar conclusions, identifying the gene in ~30% of terrestrial and freshwater species, and only one of the 739 marine cyanobacterial genomes and MAGs. Additionally, Nostoc punctiforme, a model cyanobacterium, produces the greatest amount of 2-methylhopanoids when differentiated into akinetes. These cold- and dessication-resistant cell structures are dormant and therefore not photosynthetically active, further challenging the association between 2-methylhopanes and oxygenic photosynthesis.

Other interpretations
Research demonstrating that the nitrite-oxidizing bacteria (NOB) Nitrobacter vulgaris increases its production of 2-methylhopanoids 33-fold when supplemented with cobalamin has furthered a non-cyanobacterial explanation for the observed abundance of 2-methylhopanes associated with Cretaceous OAEs. Felix Elling and colleagues propose that overturning circulation brought ammonia- and cobalt-rich deep waters to the surface, promoting aerobic nitrite oxidation and cobalamin synthesis, respectively. This model also addresses the conspicuous lack of 2-methylhopanes associated with Mediterranean sapropel events and in modern Black Sea sediments. Because both environments feature much less upwelling, 2-methylhopanoid-producing NOB such as N. vulgaris are outcompeted by NOB with higher nitrite affinity and anammox bacteria.

An environmental survey by Jessica Ricci and coauthors using metagenomes and clone libraries found significant correlation between plant-associated microbial communities and hpnP presence, based on which they propose that 2-methylhopanoids are a biomarker for sessile microbial communities high in osmolarity and low in oxygen and fixed nitrogen.

3-methylhopanoids
3-methylhopanoids have historically been associated with aerobic methanotrophy based on culture experiments and co-occurence with aerobic methanotrophs in the environment. As such, the presence of 3-methylhopanes, together with 13C depletion, are considered markers of ancient aerobic methanotrophy. However, acetic acid bacteria have been known for decades to also produce 2-methylhopanoids. Additionally, following their identification of hpnR, the gene responsible for methylating hopanoids at the C3 position, Paula Welander and Roger Summons identified putative hpnR homologs in members of alpha-, beta-, and gammaproteobacteria, actinobacteria, nitrospirae, candidate phylum NC10, and an acidobacterium, as well as in three metagenomes. As such, Welander and Summons conclude that 3-methylhopanoids alone cannot constitute evidence of aerobic methanotrophy.