
Hopanoids are a diverse subclass of
triterpenoids with the same hydrocarbon skeleton as the compound
hopane
Hopane is a natural chemical compound classified as a triterpene. It forms the central core of a variety of other chemical compounds which are collectively known as hopanoids. The first compound of the hopane family to be isolated and characte ...
. This group of
pentacyclic molecules therefore refers to simple hopenes, hopanols and hopanes, but also to extensively functionalized derivatives such as
bacteriohopanepolyols (BHPs) and hopanoids covalently attached to
lipid A
Lipid A is a lipid component of an endotoxin held responsible for the toxicity of gram-negative bacteria. It is the innermost of the three regions of the lipopolysaccharide (LPS), also called endotoxin molecule, and its hydrophobic nature allows ...
.
The first known hopanoid, hydroxyhopanone, was isolated by two chemists at
The National Gallery, London
The National Gallery is an art museum in Trafalgar Square in the City of Westminster, in Central London, England. Founded in 1824, it houses a collection of more than 2,300 paintings dating from the mid-13th century to 1900. The current dire ...
working on the chemistry of
dammar gum, a natural resin used as a varnish for paintings. While hopanoids are often assumed to be made only in bacteria, their name actually comes from the abundance of hopanoid compounds in the resin of plants from the genus ''
Hopea
''Hopea'' is a genus of plants in the family Dipterocarpaceae. It contains some 113 species, distributed from Sri Lanka and southern India to the Andaman Islands, Myanmar, southern China, and southward throughout Malesia to New Guinea. They are ...
''. In turn, this genus is named after
John Hope, the first
Regius Keeper of the
Royal Botanic Garden, Edinburgh
The Royal Botanic Garden Edinburgh (RBGE) is a scientific centre for the study of plants, their diversity and conservation, as well as a popular tourist attraction. Founded in 1670 as a physic garden to grow medicinal plants, today it occupies ...
.
Since their initial discovery in an
angiosperm
Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (). The term angiosperm is derived from the Greek words (; 'container, vessel') and (; 'seed'), meaning that the seeds are enclosed within a fruit ...
, hopanoids have been found in plasma membranes of
bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
,
lichen
A lichen ( , ) is a hybrid colony (biology), colony of algae or cyanobacteria living symbiotically among hypha, filaments of multiple fungus species, along with yeasts and bacteria embedded in the cortex or "skin", in a mutualism (biology), m ...
s,
bryophyte
Bryophytes () are a group of embryophyte, land plants (embryophytes), sometimes treated as a taxonomic Division (taxonomy), division referred to as Bryophyta ''Sensu#Common qualifiers, sensu lato'', that contains three groups of non-vascular pla ...
s,
fern
The ferns (Polypodiopsida or Polypodiophyta) are a group of vascular plants (plants with xylem and phloem) that reproduce via spores and have neither seeds nor flowers. They differ from mosses by being vascular, i.e., having specialized tissue ...
s, tropical trees and
fungi
A fungus (: fungi , , , or ; or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified as one ...
.
Hopanoids have stable
polycyclic structures that are well-preserved in
petroleum reservoir
A petroleum reservoir or oil and gas reservoir is a subsurface accumulation of hydrocarbons contained in porous or fractured rock formations. Such reservoirs form when kerogen (ancient plant matter) is created in surrounding rock by the prese ...
s, rocks and sediment, allowing the
diagenetic products of these molecules to be interpreted as
biomarker
In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, ...
s for the presence of specific microbes and potentially for chemical or physical conditions at the time of
deposition. Hopanoids have not been detected in
archaea
Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...
.
Biological function
About 10% of sequenced bacterial
genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
s have a putative ''shc'' gene encoding a
squalene-hopene cyclase and can presumably make hopanoids, which have been shown to play diverse roles in the
plasma membrane
The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extr ...
and may allow some organisms to adapt in extreme environments.
Since hopanoids modify plasma membrane properties in bacteria, they are frequently compared to
sterol
A sterol is any organic compound with a Skeletal formula, skeleton closely related to Cholestanol, cholestan-3-ol. The simplest sterol is gonan-3-ol, which has a formula of , and is derived from that of gonane by replacement of a hydrogen atom on ...
s (e.g.,
cholesterol
Cholesterol is the principal sterol of all higher animals, distributed in body Tissue (biology), tissues, especially the brain and spinal cord, and in Animal fat, animal fats and oils.
Cholesterol is biosynthesis, biosynthesized by all anima ...
), which modulate membrane fluidity and serve other functions in
eukaryotes
The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of ...
.
Although hopanoids do not rescue sterol deficiency, they are thought to increase membrane rigidity and decrease permeability.
Also,
gammaproteobacteria
''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...
and eukaryotic organisms such as lichens and bryophytes have been shown to produce both sterols and hopanoids, suggesting these lipids may have other distinct functions.
Notably, the way hopanoids pack into the plasma membrane can change depending on what functional groups are attached. The hopanoid bacteriohopanetetrol assumes a transverse orientation in
lipid bilayer
The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes form a continuous barrier around all cell (biology), cells. The cell membranes of almost all organisms and many viruses a ...
s, but diploptene localizes between the inner and outer leaflet, presumably thickening the membrane to decrease permeability.
The hopanoid diplopterol orders membranes by interacting with
lipid A
Lipid A is a lipid component of an endotoxin held responsible for the toxicity of gram-negative bacteria. It is the innermost of the three regions of the lipopolysaccharide (LPS), also called endotoxin molecule, and its hydrophobic nature allows ...
, a common membrane lipid in bacteria, in ways similar to how cholesterol and
sphingolipid
Sphingolipids are a class of lipids containing a backbone of sphingoid bases, which are a set of aliphatic amino alcohols that includes sphingosine. They were discovered in brain extracts in the 1870s and were named after the mythological sp ...
s interact in eukaryotic plasma membranes.
Diplopterol and cholesterol were demonstrated to promote condensation and inhibit gel-phase formation in both
sphingomyelin
Sphingomyelin (SPH, ) is a type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath that surrounds some nerve cell axons. It usually consists of phosphocholine and ceramide, or a phosphoethanolamine hea ...
monolayer
A monolayer is a single, closely packed layer of entities, commonly atoms or molecules.
Monolayers can also be made out of cells. ''Self-assembled monolayers'' form spontaneously on surfaces. Monolayers of layered crystals like graphene and molyb ...
s and monolayers of glycan-modified lipid A. Furthermore, both diplopterol and cholesterol could rescue pH-dependent phase transitions in glycan-modified lipid A monolayers.
The role of hopanoids in membrane-mediated acid tolerance is further supported by observations of acid-inhibited growth and morphological abnormalities of the plasma membrane in hopanoid-deficient bacteria with mutant squalene-hopene cyclases.
Hopanoids are produced in several
nitrogen-fixing bacteria
Diazotrophs are organisms capable of nitrogen fixation, i.e. converting the relatively inert diatomic nitrogen (N2) in Earth's atmosphere into bioavailable compound forms such as ammonia. Diazotrophs are typically microorganisms such as bacteria ...
.
In the
actinomycete ''
Frankia
''Frankia'' is a genus of nitrogen-fixing bacteria that live in symbiosis with actinorhizal plants, similar to the '' Rhizobium'' bacteria found in the root nodules of legumes in the family Fabaceae. ''Frankia'' also initiate the forming of ro ...
'', hopanoids in the membranes of
vesicles
Vesicle may refer to:
; In cellular biology or chemistry
* Vesicle (biology and chemistry), a supramolecular assembly of lipid molecules, like a cell membrane
* Synaptic vesicle
In a neuron, synaptic vesicles (or neurotransmitter vesicles) s ...
specialized for
nitrogen fixation
Nitrogen fixation is a chemical process by which molecular dinitrogen () is converted into ammonia (). It occurs both biologically and abiological nitrogen fixation, abiologically in chemical industry, chemical industries. Biological nitrogen ...
likely restrict the entry of
oxygen
Oxygen is a chemical element; it has chemical symbol, symbol O and atomic number 8. It is a member of the chalcogen group (periodic table), group in the periodic table, a highly reactivity (chemistry), reactive nonmetal (chemistry), non ...
by making the lipid bilayer more tight and compact. In ''
Bradyrhizobium
''Bradyrhizobium'' is a genus of Gram-negative bacteria, Gram-negative soil bacteria, many of which fix nitrogen. Nitrogen fixation is an important part of the nitrogen cycle. Plants cannot use atmospheric nitrogen (N2); they must use nitrogen co ...
'', hopanoids chemically bonded to lipid A increase membrane stability and rigidity, enhancing stress tolerance and intracellular survival in ''
Aeschynomene
''Aeschynomene'' is a genus of flowering plants in the family Fabaceae, and was recently assigned to the informal monophyly, monophyletic ''Dalbergia'' clade of the Dalbergieae. They are known commonly as jointvetches. They range across tropical ...
''
legume
Legumes are plants in the pea family Fabaceae (or Leguminosae), or the fruit or seeds of such plants. When used as a dry grain for human consumption, the seeds are also called pulses. Legumes are grown agriculturally, primarily for human consum ...
s. In the
cyanobacterium
Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteria' ...
''
Nostoc punctiforme'', large quantities of 2-methylhopanoids localize to the outer membranes of survival structures called
akinete
An akinete is an enveloped, thick-walled, non-motile, dormant cell (biology), cell formed by both cyanobacteria and algae. Cyanobacterial akinetes are mainly formed by filamentous, heterocyst-forming members under the order Nostocales and Stigone ...
s.
In another example of stress tolerance, hopanoids in the aerial
hyphae
A hypha (; ) is a long, branching, filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium.
Structure
A hypha consists of one o ...
(spore bearing structures) of the prokaryotic soil bacteria ''
Streptomyces
''Streptomyces'', from στρεπτός (''streptós''), meaning "twisted", and μύκης (''múkés''), meaning "fungus", is the largest genus of Actinomycetota, and the type genus of the family Streptomycetaceae. Over 700 species of ''St ...
'' are thought to minimize water loss across the membrane to the air.
Biosynthesis
Squalene synthesis
Since hopanoids are a C
30 terpenoid, biosynthesis begins with
isopentenyl pyrophosphate
Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP) is an isoprenoid precursor. IPP is an intermediate in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway) and in the ''non-mevalonate'' MEP pathway of i ...
(IPP) and
dimethylallyl pyrophosphate
Dimethylallyl pyrophosphate (DMAPP; or alternatively, dimethylallyl diphosphate (DMADP); also isoprenyl pyrophosphate) is an isoprenoid precursor. It is a product of both the mevalonate pathway and the MEP pathway of isoprenoid precursor biosynt ...
(DMAP), which are combined to form longer chain
isoprenoids
The terpenoids, also known as isoprenoids, are a class of naturally occurring organic chemicals derived from the 5-carbon compound isoprene and its derivatives called terpenes, diterpenes, etc. While sometimes used interchangeably with "terpenes" ...
.
Synthesis of these smaller precursors proceeds either via the
mevalonate pathway
The mevalonate pathway, also known as the isoprenoid pathway or HMG-CoA reductase pathway is an essential metabolic pathway present in eukaryotes, archaea, and some bacteria. The pathway produces two five-carbon building blocks called isopentenyl ...
or the
methylerythritol-4-phosphate pathway depending on the bacterial species, although the latter tends to be more common. DMAP condenses with one molecule of IPP to
geranyl pyrophosphate
Geranyl pyrophosphate (GPP), also known as geranyl diphosphate (GDP), is the pyrophosphate ester of the terpenoid geraniol. Its salts are colorless. It is a precursor to many thousands of natural product, natural products.
Occurrence
GPP is an int ...
, which in turn condenses with another IPP to generate
farnesyl pyrophosphate (FPP).
Squalene synthase
Squalene synthase (SQS) or farnesyl-diphosphate:farnesyl-diphosphate farnesyl transferase is an enzyme localized to the membrane of the endoplasmic reticulum. SQS participates in the terpenoid, isoprenoid biosynthetic pathway, catalyzing a two-s ...
, coded for by the gene ''sqs'', then catalyzes the condensation of two FPP molecules to presqualene pyrophosphate (PSPP) before oxidizing
NADPH
Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require N ...
to release
squalene
Squalene is an organic compound. It is a triterpene with the formula C30H50. It is a colourless oil, although impure samples appear yellow. It was originally obtained from shark liver oil (hence its name, as '' Squalus'' is a genus of sharks). ...
.
However, some hopanoid-producing bacteria lack squalene synthase and instead use the three enzymes HpnC, HpnD and HpnE, which are encoded in the ''hpn'' operon with many other hopanoid biosynthesis genes. In this alternative yet seemingly more widespread squalene synthesis pathway, HpnD releases
pyrophosphate
In chemistry, pyrophosphates are phosphorus oxyanions that contain two phosphorus atoms in a linkage. A number of pyrophosphate salts exist, such as disodium pyrophosphate () and tetrasodium pyrophosphate (), among others. Often pyrophosphates a ...
as it condenses two molecules of FPP to PSPP, which HpnC converts to hydroxysqualene, consuming a water molecule and releasing another pyrophosphate. Then, hydroxysqualene is reduced to squalene in a dehydration reaction mediated by the
FAD
A fad, trend, or craze is any form of collective behavior that develops within a culture, a generation, or social group in which a group of people enthusiastically follow an impulse for a short time period.
Fads are objects or behaviors tha ...
-dependent enzyme HpnE.
Cyclization

Next, a squalene-hopene cyclase catalyzes an elaborate cyclization reaction, engaging squalene in an energetically favorable all-chair conformation before creating five cycles, six covalent bonds, and nine chiral centers on the molecule in a single step.
This enzyme, coded for by the gene ''shc (''also called ''hpnF'' in some bacteria), has a double ⍺-barrel fold characteristic of terpenoid biosynthesis and is present in the cell as a monotopic
homodimer
In biochemistry, a protein dimer is a macromolecular complex or protein multimer, multimer formed by two protein monomers, or single proteins, which are usually Non-covalent interaction, non-covalently bound. Many macromolecules, such as proteins ...
, meaning pairs of the cyclase are embedded in but do not span the plasma membrane.
''
In vitro
''In vitro'' (meaning ''in glass'', or ''in the glass'') Research, studies are performed with Cell (biology), cells or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in ...
'', this enzyme exhibits promiscuous substrate specificity, also cyclizing
2,3-oxidosqualene
(''S'')-2,3-Oxidosqualene ((''S'')-2,3-epoxysqualene) is an intermediate in the synthesis of the cell membrane sterol precursors lanosterol and cycloartenol, as well as saponins. It is formed when squalene is oxidized by the enzyme squale ...
.
Aromatic residues in the active site form several unfavorable
carbocation
Carbocation is a general term for ions with a positively charged carbon atom. In the present-day definition given by the IUPAC, a carbocation is any even-electron cation with significant partial positive charge on a carbon atom. They are further ...
s on the substrate which are quenched by a rapid polycyclization.
In the last substep of the cyclization reaction, after electrons comprising the
terminal alkene
In organic chemistry, terminal alkenes (alpha-olefins, α-olefins, or 1-alkenes) are a family of organic compounds which are alkenes (also known as olefins) with a chemical formula , distinguished by having a double bond at the primary, alpha ( ...
bond on the squalene have attacked the hopenyl carbocation to close the E ring, the C
22 carbocation may be quenched by mechanisms that lead to different hopanoid products. Nucleophilic attack of water will yield diplopterol, while deprotonation at an adjacent carbon will form one of several hopene isomers, often diploptene.
Functionalization
After cyclization, hopanoids are frequently modified by hopanoid biosynthesis enzymes encoded by genes in the same operon as ''shc'', ''hpn''. For instance, the
radical SAM
Radical SAM enzymes belong to a superfamily of enzymes that use an iron-sulfur cluster (4Fe-4S) to reductively cleave S-Adenosyl methionine, ''S''-adenosyl-L-methionine (SAM) to generate a radical (chemistry), radical, usually a 5′-deoxyadenosyl ...
protein HpnH adds an
adenosine
Adenosine (symbol A) is an organic compound that occurs widely in nature in the form of diverse derivatives. The molecule consists of an adenine attached to a ribose via a β-N9- glycosidic bond. Adenosine is one of the four nucleoside build ...
group to diploptene, forming the extended C
35 hopanoid adenosylhopane, which can then be further functionalized by other ''hpn'' gene products. HpnG catalyzes the removal of
adenine
Adenine (, ) (nucleoside#List of nucleosides and corresponding nucleobases, symbol A or Ade) is a purine nucleotide base that is found in DNA, RNA, and Adenosine triphosphate, ATP. Usually a white crystalline subtance. The shape of adenine is ...
from adenosylhopane to make ribosyl hopane, which reacts to form bacteriohopanetetrol (BHT) in a reaction mediated by an unknown enzyme. Additional modifications may occurs as HpnO aminates the terminal hydroxyl on BHT, producing amino bacteriohopanetriol, or as the
glycosyltransferase
Glycosyltransferases (GTFs, Gtfs) are enzymes ( EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic gl ...
HpnI converts BHT to N-acetylglucosaminyl-BHT.
In sequence, the hopanoid biosynthesis associated protein HpnK mediates deacetylation to glucosaminyl-BHT, from which radical SAM protein HpnJ generates a
cyclitol
In organic chemistry, a cyclitol is a cycloalkane containing at least three hydroxyl, each attached to a different ring carbon atom. The general formula for an unsubstituted cyclitol is or where 3 ≤ ''x'' ≤ ''n''.
The name is also used for ...
ether.
Importantly, C
30 and C
35 hopanoids alike may be methylated at C
2 and C
3 positions by the radical SAM
methyltransferases HpnP and HpnR, respectively.
These two methylations are particularly geostable compared to side-chain modifications and have entertained geobiologists for decades.
In a biosynthetic pathway exclusive to some bacteria, the enzyme tetrahymanol synthase catalyzes the conversion of the hopanoid diploptene to the pentacyclic triterpenoid
tetrahymanol. In eukaryotes like ''
Tetrahymena
''Tetrahymena'' is a genus of free-living ciliates, examples of unicellular eukaryotes. The genus Tetrahymena is the most widely studied member of its phylum. It can produce, store and react with different types of hormones. ''Tetrahymena'' cel ...
'', tetrahymanol is instead synthesized directly from squalene by a cyclase with no homology to the bacterial tetrahymanol synthase.
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. The total amount in the Earth was estimated as 10 x 10
18 gram (10
12 ton) in 1992. Biomolecules like DNA and proteins are degraded during
diagenesis
Diagenesis () is the process of physical and chemical changes in sediments first caused by water-rock interactions, microbial activity, and compaction after their deposition. Increased pressure and temperature only start to play a role as sedi ...
, 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
sterane
Steranes constitute a group of alkane organic compounds with a cyclopentane-fused hydrogenated phenanthrene structure as the parent nucleus, and they derived from steroids or sterols via diagenetic and catagenetic degradation, such as hydrogen ...
s 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
The Mesoproterozoic Era is a geologic era that occurred from . The Mesoproterozoic was the first era of Earth's history for which a fairly definitive geological record survives. Continents existed during the preceding era (the Paleoproterozoic ...
okenanes, steranes, and methylhopanes from a 1.64
Ga (billion year) old basin in Australia. However,
molecular clock
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleot ...
analyses estimate that the earliest sterols were likely produced around 2.3 Ga ago, around the same time as the
Great Oxidation Event
The Great Oxidation Event (GOE) or Great Oxygenation Event, also called the Oxygen Catastrophe, Oxygen Revolution, Oxygen Crisis or Oxygen Holocaust, was a time interval during the Earth's Paleoproterozoic era when the Earth's atmosphere an ...
, 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
Squalene monooxygenase (also called squalene epoxidase) is a eukaryotic enzyme that uses NADPH and diatomic oxygen to oxidize squalene to 2,3-oxidosqualene (squalene epoxide). Squalene epoxidase catalyzes the first oxygenation step in sterol b ...
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.
2-methylhopanoids
As a biomarker for cyanobacteria
= Proposal
=
2-methylhopanes, often quantified as the 2-α-methylhopane index, were first proposed as a biomarker for
oxygenic photosynthesis
Photosynthesis ( ) is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metaboli ...
by
Roger Summons and colleagues following the discovery of the precursor lipids, 2-methylhopanols, in
cyanobacteria
Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
l cultures and mats. The subsequent discovery of 2-α-methylhopanes supposedly from
photosynthetic
Photosynthesis ( ) is a Biological system, system of biological processes by which Photoautotrophism, photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical ener ...
cyanobacteria
Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
in 2.7 Ga old
shale
Shale is a fine-grained, clastic sedimentary rock formed from mud that is a mix of flakes of Clay mineral, clay minerals (hydrous aluminium phyllosilicates, e.g., Kaolinite, kaolin, aluminium, Al2Silicon, Si2Oxygen, O5(hydroxide, OH)4) and tiny f ...
s from the
Pilbara Craton of Western Australia suggested a 400
Ma (million year) gap between the evolution of oxygenic metabolism and the Great Oxidation Event. However, these findings were later rejected due to potential contamination by modern hydrocarbons.
Putative cyanobacterial presence on the basis of abundant 2-methylhopanes has been used to explain black shale deposition during
Aptian
The Aptian is an age (geology), age in the geologic timescale or a stage (stratigraphy), stage in the stratigraphic column. It is a subdivision of the Early Cretaceous, Early or Lower Cretaceous epoch (geology), Epoch or series (stratigraphy), S ...
and
Cenomanian–Turonian Ocean Anoxic Events (OAEs) and the associated
15N isotopic signatures indicative of N
2-fixation. In contrast, 2-α-methylhopane index values are relatively low across similar
Frasnian
The Frasnian is one of two faunal stages in the Late Devonian Period. It lasted from million years ago to million years ago. It was preceded by the Givetian Stage and followed by the Famennian Stage.
Major reef-building was under way during ...
and
Famennian
The Famennian is the later of two faunal stages in the Late Devonian epoch. The most recent estimate for its duration is that it lasted from around 371.1 to 359.3 million years ago. An earlier 2012 estimate, still used by the International Commis ...
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-methyl-hopanols, when grown under strictly anaerobic conditions.
Furthermore, the anoxygenic
phototroph
Phototrophs () are organisms that carry out photon capture to produce complex organic compounds (e.g. carbohydrates) and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a list of common m ...
''
Rhodopseudomonas palustris'' was found to produce 2-methyl-BHPs only under anoxic conditions. 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
''Alphaproteobacteria'' or ''α-proteobacteria'', also called ''α-Purple bacteria'' in earlier literature, is a class of bacteria in the phylum '' Pseudomonadota'' (formerly "Proteobacteria"). The '' Magnetococcales'' and '' Mariprofundales'' ar ...
, and phylogenetic analysis of the gene concluded that it originated in the alphaproteobacteria and was acquired by the cyanobacteria and
acidobacteriota
Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.
Description
Members of this phylum are physiologically diverse, and can be ...
via
horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the e ...
.
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'' produces the greatest amount of 2-methylhopanoids when differentiated into
akinete
An akinete is an enveloped, thick-walled, non-motile, dormant cell (biology), cell formed by both cyanobacteria and algae. Cyanobacterial akinetes are mainly formed by filamentous, heterocyst-forming members under the order Nostocales and Stigone ...
s. These cold- and desiccation-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
Vitamin B12, also known as cobalamin, is a water-soluble vitamin involved in metabolism. One of eight B vitamins, it serves as a vital cofactor (biochemistry), cofactor in DNA synthesis and both fatty acid metabolism, fatty acid and amino a ...
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
The Mediterranean Sea ( ) is a sea connected to the Atlantic Ocean, surrounded by the Mediterranean basin and almost completely enclosed by land: on the east by the Levant in West Asia, on the north by Anatolia in West Asia and Southern ...
sapropel
Sapropel (a contraction of Ancient Greek words ''sapros'' and ''pelos'', meaning putrefaction and mud (or clay), respectively) is a term used in marine geology to describe dark-coloured sediments that are rich in organic matter. Organic carbon conc ...
events and in modern
Black Sea
The Black Sea is a marginal sea, marginal Mediterranean sea (oceanography), mediterranean sea lying between Europe and Asia, east of the Balkans, south of the East European Plain, west of the Caucasus, and north of Anatolia. It is bound ...
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
Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a gr ...
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
methanotroph
Methanotrophs (sometimes called methanophiles) are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to ...
y based on culture experiments
and co-occurrence 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
Acetic acid bacteria (AAB) are a group of Gram-negative bacteria which Oxidation, oxidize sugars or ethanol and produce acetic acid during Aerobic fermentation, fermentation. The acetic acid bacteria consist of 10 genus, genera in the family Acet ...
have been known for decades to also produce 2-methylhopanoids.
Additionally, following their identification of ''hpnR'', the gene responsible for methylating hopanoids at the C
3 position,
Paula Welander and
Roger Summons identified putative ''hpnR'' homologs in members of
alpha
Alpha (uppercase , lowercase ) is the first letter of the Greek alphabet. In the system of Greek numerals, it has a value of one. Alpha is derived from the Phoenician letter ''aleph'' , whose name comes from the West Semitic word for ' ...
-,
beta
Beta (, ; uppercase , lowercase , or cursive ; or ) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Ancient Greek, beta represented the voiced bilabial plosive . In Modern Greek, it represe ...
-, and
gammaproteobacteria
''Gammaproteobacteria'' is a class of bacteria in the phylum ''Pseudomonadota'' (synonym ''Proteobacteria''). It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. Several medically, ecologically, and scienti ...
,
actinomycetota
The Actinomycetota (or Actinobacteria) are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great importance to land flora because of their contributions to soil systems. In soil t ...
,
nitrospirota
The Nitrospirota are a phylum of bacteria. They include multiple genera such as '' Nitrospira'', the largest.
History of knowledge
The first member of this phylum, '' Nitrospira marina'', was discovered in 1985. The second member, '' Nitrospi ...
,
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.
Applications
Industry
The elegant mechanism behind the protonase activity of squalene-hopene cyclase was appreciated and adapted by chemical engineers at the University of Stuttgart, Germany. Active site engineering resulted in loss of the enzyme's ability to form hopanoids, but enabled
Brønsted acid catalysis for the
stereoselective cyclization of the
monoterpenoids geraniol
Geraniol is a monoterpenoid and an alcohol. It is the primary component of citronella oil and is a primary component of rose oil and palmarosa oil. It is a colorless oil, although commercial samples can appear yellow. It has low solubility i ...
, epoxygeraniol, and
citronellal.
Agriculture
The application of hopanoids and hopanoid-producing nitrogen fixers to soil has been proposed and patented as a biofertilizer technique that increases environmental resistance of plant-associated microbial symbionts, including nitrogen-fixing bacteria that are essential for transforming atmospheric nitrogen to soluble forms available to crops.
Medicine
During later studies of interactions between diplopterol and lipid A in ''
Methylobacterium extorquens'', multidrug transport was found to be a hopanoid-dependent process. Squalene-hopene cyclase mutants derived from a wild type capable of
multidrug efflux, a drug-resistance mechanism mediated by integral transport proteins, lost the ability to perform both multidrug transport and hopanoid synthesis.
Researchers indicate this could be due to direct regulation of transport proteins by hopanoids or indirectly by altering membrane ordering in a way that disrupts the transport system.
References
{{Reflist
Triterpenes
Membrane biology
Bacteria
Microbiology