Jacob R. Waldbauer

The carbon cycle and associated redox processes through time

Earths biogeochemical cycle of carbon delivers both limestones and organic materials to the crust. In numerous, biologically catalysed redox reactions, hydrogen, sulphur, iron, and oxygen serve prominently as electron donors and acceptors. The progress of these reactions can be reconstructed from records of variations in the abundance of 13C in sedimentary carbonate minerals and organic materials. Because the crust is always receiving new CO2 from the mantle and a portion of it is being reduced by photoautotrophs, the carbon cycle has continuously released oxidizing power. Most of it is represented by Fe3+ that has accumulated in the crust or been returned to the mantle via subduction. Less than 3% of the estimated, integrated production of oxidizing power since 3.8 Gyr ago is represented by O2 in the atmosphere and dissolved in seawater. The balance is represented by sulphate. The accumulation of oxidizing power can be estimated from budgets summarizing inputs of mantle carbon and rates of organic-carbon burial, but levels of O2 are only weakly and indirectly coupled to those phenomena and thus to carbon-isotopic records. Elevated abundances of 13C in carbonate minerals ca 2.3 Gyr old, in particular, are here interpreted as indicating the importance of methanogenic bacteria in sediments rather than increased burial of organic carbon.

Steroids, triterpenoids and molecular oxygen.

There is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. Thus, the detection of steroid and triterpenoid hydrocarbons far back in Earth history has been used to infer the antiquity of oxygenic photosynthesis. This prompts the question: were these compounds produced similarly in the past? In this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requirement for steroid biosynthesis and phylogenetic patterns in the distribution of steroid and triterpenoid biosynthetic pathways. The hopanoid and steroid biosynthetic pathways are very highly conserved within the bacterial and eukaryotic domains, respectively. Bacteriohopanepolyols are produced by a wide range of bacteria, and are methylated in significant abundance at the C2 position by oxygen-producing cyanobacteria. On the other hand, sterol biosynthesis is sparsely distributed in distantly related bacterial taxa and the pathways do not produce the wide range of products that characterize eukaryotes. In particular, evidence for sterol biosynthesis by cyanobacteria appears flawed. Our experiments show that cyanobacterial cultures are easily contaminated by sterol-producing rust fungi, which can be eliminated by treatment with cycloheximide affording sterol-free samples. Sterols are ubiquitous features of eukaryotic membranes, and it appears likely that the initial steps in sterol biosynthesis were present in their modern form in the last common ancestor of eukaryotes. Eleven molecules of O2 are required by four enzymes to produce one molecule of cholesterol. Thermodynamic arguments, optimization of function and parsimony all indicate that an ancestral anaerobic pathway is highly unlikely. The known geological record of molecular fossils, especially steranes and triterpanes, is notable for the limited number of structural motifs that have been observed. With a few exceptions, the carbon skeletons are the same as those found in the lipids of extant organisms and no demonstrably extinct structures have been reported. Furthermore, their patterns of occurrence over billion year time-scales correlate strongly with environments of deposition. Accordingly, biomarkers are excellent indicators of environmental conditions even though the taxonomic affinities of all biomarkers cannot be precisely specified. Biomarkers are ultimately tied to biochemicals with very specific functional properties, and interpretations of the biomarker record will benefit from increased understanding of the biological roles of geologically durable molecules.

The Geological Succession of Primary Producers in the Oceans

Publisher Summary This chapter explores two records of past primary producers: morphological fossils and molecular biomarkers. Because these two windows on ancient biology are framed by such different patterns of preservational bias and diagenetic selectivity, they are likely to present a common picture of stratigraphic variation only if that view reflects evolutionary history. Diagenesis can obliterate fossils as well as preserve them: organic walls are subject to postdepositional oxidation and mineralized skeletons may dissolve in undersaturated pore waters. The molecular and morphological records of eukaryotic predominance in shelf primary production are mirrored by indications of relatively low cyanobacterial contributions. Fossils, molecular biomarkers, molecular clocks for individual clades, and the sedimentary silica record all disclose that the modern phytoplankton has Mesozoic roots. Paleozoic primary production is described in detail. Microfossil and biomarker molecules both suggest that green algae played a greater role in marine primary production than they have in the past 100 million years, and biomarkers also suggest a significant role for cyanobacterial production on continental shelves. The later part of the chapterdiscusses about proterozoic primary production and also explains the prokaryotic fossils, eukaryotic fossils, and proterozoic molecular biomarkers. The chapter concludes that improved understanding of Earths redox history and the evolutionary record of animals and land plants will provide the framework needed to interpret the evolutionary history of marine photoautotrophs as it continues to emerge.

Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host.

Proteorhodopsins (PRs) are retinal-containing proteins that catalyze light-activated proton efflux across the cell membrane. These photoproteins are known to be globally distributed in the oceans photic zone, and they are found in a diverse array of Bacteria and Archaea. Recently, light-enhanced growth rates and yields have been reported in at least one PR-containing marine bacterium, but the physiological basis of light-activated growth stimulation has not yet been determined. To describe more fully PR photosystem genetics and biochemistry, we functionally surveyed a marine picoplankton large-insert genomic library for recombinant clones expressing PR photosystems in vivo. Our screening approach exploited transient increases in vector copy number that significantly enhanced the sensitivity of phenotypic detection. Two genetically distinct recombinants, initially identified by their orange pigmentation, expressed a small cluster of genes encoding a complete PR-based photosystem. Genetic and biochemical analyses of transposon mutants verified the function of gene products in the photopigment and opsin biosynthetic pathways. Heterologous expression of six genes, five encoding photopigment biosynthetic proteins and one encoding a PR, generated a fully functional PR photosystem that enabled photophosphorylation in recombinant Escherichia coli cells exposed to light. Our results demonstrate that a single genetic event can result in the acquisition of phototrophic capabilities in an otherwise chemoorganotrophic microorganism, and they explain in part the ubiquity of PR photosystems among diverse microbial taxa.

Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters

Prochlorococcus and Synechococcus are the two most abundant marine cyanobacteria. They represent a significant fraction of the total primary production of the world oceans and comprise a major fraction of the prey biomass available to phagotrophic protists. Despite relatively rapid growth rates, picocyanobacterial cell densities in open-ocean surface waters remain fairly constant, implying steady mortality due to viral infection and consumption by predators. There have been several studies on grazing by specific protists on Prochlorococcus and Synechococcus in culture, and of cell loss rates due to overall grazing in the field. However, the specific sources of mortality of these primary producers in the wild remain unknown. Here, we use a modification of the RNA stable isotope probing technique (RNA-SIP), which involves adding labelled cells to natural seawater, to identify active predators that are specifically consuming Prochlorococcus and Synechococcus in the surface waters of the Pacific Ocean. Four major groups were identified as having their 18S rRNA highly labelled: Prymnesiophyceae (Haptophyta), Dictyochophyceae (Stramenopiles), Bolidomonas (Stramenopiles) and Dinoflagellata (Alveolata). For the first three of these, the closest relative of the sequences identified was a photosynthetic organism, indicating the presence of mixotrophs among picocyanobacterial predators. We conclude that the use of RNA-SIP is a useful method to identity specific predators for picocyanobacteria in situ, and that the method could possibly be used to identify other bacterial predators important in the microbial food-web.

Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle

Background Growth of the oceans most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotrophs highly choreographed response to the daily oscillation in energy supply. Methodology/Principal Findings Using RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle. These temporal expression patterns reveal strong oscillations in transcript abundance that are broadly damped at the protein level, with mRNA levels varying on average 2.3 times more than the corresponding protein. The single strongest observed protein-level oscillation is in a ribonucleotide reductase, which may reflect a defense strategy against phage infection. The peak in abundance of most proteins also lags that of their transcript by 2–8 hours, and the two are completely antiphase for some genes. While abundant antisense RNA was detected, it apparently does not account for the observed divergences between expression levels. The redirection of flux through central carbon metabolism from daytime carbon fixation to nighttime respiration is associated with quite small changes in relative enzyme abundances. Conclusions/Significance Our results indicate that expression responses to periodic stimuli that are common in natural ecosystems (such as the diel cycle) can diverge significantly between the mRNA and protein levels. Protein expression patterns that are distinct from those of cognate mRNA have implications for the interpretation of transcriptome and metatranscriptome data in terms of cellular metabolism and its biogeochemical impact.

Microaerobic steroid biosynthesis and the molecular fossil record of Archean life

The power of molecular oxygen to drive many crucial biogeochemical processes, from cellular respiration to rock weathering, makes reconstructing the history of its production and accumulation a first-order question for understanding Earth’s evolution. Among the various geochemical proxies for the presence of O2 in the environment, molecular fossils offer a unique record of O2 where it was first produced and consumed by biology: in sunlit aquatic habitats. As steroid biosynthesis requires molecular oxygen, fossil steranes have been used to draw inferences about aerobiosis in the early Precambrian. However, better quantitative constraints on the O2 requirement of this biochemistry would clarify the implications of these molecular fossils for environmental conditions at the time of their production. Here we demonstrate that steroid biosynthesis is a microaerobic process, enabled by dissolved O2 concentrations in the nanomolar range. We present evidence that microaerobic marine environments (where steroid biosynthesis was possible) could have been widespread and persistent for long periods of time prior to the earliest geologic and isotopic evidence for atmospheric O2. In the late Archean, molecular oxygen likely cycled as a biogenic trace gas, much as compounds such as dimethylsulfide do today.

Deciphering ocean carbon in a changing world

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.

Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli.

High translational fidelity is commonly considered a requirement for optimal cellular health and protein function. However, recent findings have shown that inducible mistranslation specifically with methionine engendered at the tRNA charging level occurs in mammalian cells, yeast and archaea, yet it was unknown whether bacteria were capable of mounting a similar response. Here, we demonstrate that Escherichia coli misacylates non-methionyl-tRNAs with methionine in response to anaerobiosis and antibiotic exposure via the methionyl–tRNA synthetase (MetRS). Two MetRS succinyl-lysine modifications independently confer high tRNA charging fidelity to the otherwise promiscuous, unmodified enzyme. Strains incapable of tRNA mismethionylation are less adept at growth in the presence of antibiotics and stressors. The presence of tRNA mismethionylation and its potential role in mistranslation within the bacterial domain establishes this response as a pervasive biological mechanism and connects it to diverse cellular functions and modes of fitness.

Postnovo: Post-Processing Enables Accurate and FDR-Controlled De Novo Peptide Sequencing

De novo sequencing offers an alternative to database search methods for peptide identification from mass spectra. Since it does not rely on a predetermined database of expected or potential sequences in the sample, de novo sequencing is particularly appropriate for samples lacking a well-defined or comprehensive reference database. However, the low accuracy of many de novo sequence predictions has prevented the widespread use of the variety of sequencing tools currently available. Here, we present a new open-source tool, Postnovo, that postprocesses de novo sequence predictions to find high-accuracy results. Postnovo uses a predictive model to rescore and rerank candidate sequences in a manner akin to database search postprocessing tools such as Percolator. Postnovo leverages the output from multiple de novo sequencing tools in its own analyses, producing many times the length of amino acid sequence information (including both full- and partial-length peptide sequences) at an equivalent false discovery rate (FDR) compared to any individual tool. We present a methodology to reliably screen the sequence predictions to a desired FDR given the Postnovo sequence score. We validate Postnovo with multiple data sets and demonstrate its ability to identify proteins that are missed by database search even in samples with paired reference databases.