Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

Abstract

Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

Synthesis of arborane triterpenols by a bacterial oxidosqualene cyclase

“…Bioinformatics coupled to lipid analyses and protein characterization have contributed significantly to our understanding of the taxonomic distribution of microbial lipid biomarkers, the enzymatic mechanisms of their synthesis, and the potential evolutionary relationships of their biosynthetic pathways (39). Here, this combined approach revealed two triterpenols that not only address a current incongruity in biomarker signatures but also provide mechanistic insight into polycyclic triterpenoid biosynthesis.…”

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

“…EdgeR analysis indicated that as much as 10.1% in the Arctic and 10.6% in the Antarctica of total differentially expressed genes after 24 h of ADOC exposure belonged to cell wall and membrane transport SEED categories, just below SEED categories related to cell growth (carbohydrates, amino acids and protein metabolism; Supporting Information Fig. We identified three main bacterial strategies to decrease ADOC adverse effects on cells, other than degradation, based on our results and literature search: (i) modification of membrane rigidity/viscosity and permeability by remodelling membrane composition (Kabelitz et al, 2003;Newman et al, 2016), (ii) export of lipid substances outside the cell (Sharom, 2014) and (iii) production of extracellular polymeric substances (EPSs) and biosurfactants to modify the cell surface (Shao et al, 2017). For instance, lipid modification in the Arctic and colanic acid biosynthesis in Antarctica was the most differentially expressed genes in the community, indicating reshaping of membranes and cell walls.…”

“…Flavobacteriia and other bacteria dominated the FA desaturase Pfam that was particularly expressed in Arctic ADOC amendments after 24 h (Fig. 4; Garneau et al, 2016;Newman et al, 2016;Vergeynst et al, 2018). In order to track the second mechanism, we quantified the number of transcripts of isoprenoid biosynthesis, as hopanoids (triterpenes) are synthesized from isoprene.…”

Hopanoid lipids: from membranes to plant–bacteria interactions

“…It is therefore difficult to attribute hopanes in the rock record to the advent of a specific phylogenetic group, metabolic process or environmental context. Reviews of the efforts to interpret hopanoids in the rock record are available in the literature 8,9 .…”