110 research outputs found
Light-driven oxidation of polysaccharides by photosynthetic pigments and a metalloenzyme
Oxidative processes are essential for the degradation of plant biomass. A class of powerful and widely distributed oxidative enzymes, the lytic polysaccharide monooxygenases (LPMOs), oxidize the most recalcitrant polysaccharides and require extracellular electron donors. Here we investigated the effect of using excited photosynthetic pigments as electron donors. LPMOs combined with pigments and reducing agents were exposed to light, which resulted in a never before seen 100-fold increase in catalytic activity. In addition, LPMO substrate specificity was broadened to include both cellulose and hemicellulose. LPMO enzymes and pigment derivatives common in the environment of plant-degrading organisms thus form a highly reactive and stable light-driven system increasing the turnover rate and versatility of LPMOs. This light-driven system may find applications in biotechnology and chemical processing
Exciton Dynamics in Photosynthetic Complexes: Excitation by Coherent and Incoherent Light
In this paper we consider dynamics of a molecular system subjected to
external pumping by a light source. Within a completely quantum mechanical
treatment, we derive a general formula, which enables to asses effects of
different light properties on the photo-induced dynamics of a molecular system.
We show that once the properties of light are known in terms of certain
two-point correlation function, the only information needed to reconstruct the
system dynamics is the reduced evolution superoperator. The later quantity is
in principle accessible through ultrafast non-linear spectroscopy. Considering
a direct excitation of a small molecular antenna by incoherent light we find
that excitation of coherences is possible due to overlap of homogeneous line
shapes associated with different excitonic states. In Markov and secular
approximations, the amount of coherence is significant only under fast
relaxation, and both the populations and coherences between exciton states
become static at long time. We also study the case when the excitation of a
photosynthetic complex is mediated by a mesoscopic system. We find that such
case can be treated by the same formalism with a special correlation function
characterizing ultrafast fluctuations of the mesoscopic system. We discuss
bacterial chlorosom as an example of such a mesoscopic mediator and propose
that the properties of energy transferring chromophore-protein complexes might
be specially tuned for the fluctuation properties of their associated antennae.Comment: 12 page
Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium
Proteorhodopsin (PR) is a photoprotein that functions as a light-driven proton pump in diverse marine Bacteria and Archaea. Recent studies have suggested that PR may enhance both growth rate and yield in some flavobacteria when grown under nutrient-limiting conditions in the light. The direct involvement of PR, and the metabolic details enabling light-stimulated growth, however, remain uncertain. Here, we surveyed transcriptional and growth responses of a PR-containing marine flavobacterium during carbon-limited growth in the light and the dark. As previously reported (Gómez-Consarnau et al., 2007), Dokdonia strain MED134 exhibited light-enhanced growth rates and cell yields under low carbon growth conditions. Inhibition of retinal biosynthesis abolished the light-stimulated growth response, supporting a direct role for retinal-bound PR in light-enhanced growth. Among protein-coding transcripts, both PR and retinal biosynthetic enzymes showed significant upregulation in the light. Other light-associated proteins, including bacterial cryptochrome and DNA photolyase, were also expressed at significantly higher levels in the light. Membrane transporters for Na+/phosphate and Na+/alanine symporters, and the Na+-translocating NADH-quinone oxidoreductase (NQR) linked electron transport chain, were also significantly upregulated in the light. Culture experiments using a specific inhibitor of Na+-translocating NQR indicated that sodium pumping via NQR is a critical metabolic process in the light-stimulated growth of MED134. In total, the results suggested the importance of both the PR-enabled, light-driven proton gradient, as well as the generation of a Na+ ion gradient, as essential components for light-enhanced growth in these flavobacteria.Gordon and Betty Moore FoundationNational Science Foundation (U.S.) (NSF Science and Technology Center Award EF0424599.)Japan Society for the Promotion of Science (Postdoctoral Fellowships for Research Abroad
Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts
Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host–symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry
Genetic Co-Occurrence Network across Sequenced Microbes
The phenotype of any organism on earth is, in large part, the consequence of
interplay between numerous gene products encoded in the genome, and such
interplay between gene products affects the evolutionary fate of the genome
itself through the resulting phenotype. In this regard, contemporary genomes
can be used as molecular records that reveal associations of various genes
working in their natural lifestyles. By analyzing thousands of orthologs across
~600 bacterial species, we constructed a map of gene-gene co-occurrence across
much of the sequenced biome. If genes preferentially co-occur in the same
organisms, they were called herein correlogs; in the opposite case, called
anti-correlogs. To quantify correlogy and anti-correlogy, we alleviated the
contribution of indirect correlations between genes by adapting ideas developed
for reverse engineering of transcriptional regulatory networks. Resultant
correlogous associations are highly enriched for physically interacting
proteins and for co-expressed transcripts, clearly differentiating a subgroup
of functionally-obligatory protein interactions from conditional or transient
interactions. Other biochemical and phylogenetic properties were also found to
be reflected in correlogous and anti-correlogous relationships. Additionally,
our study elucidates the global organization of the gene association map, in
which various modules of correlogous genes are strikingly interconnected by
anti-correlogous crosstalk between the modules. We then demonstrate the
effectiveness of such associations along different domains of life and
environmental microbial communities. These phylogenetic profiling approaches
infer functional coupling of genes regardless of mechanistic details, and may
be useful to guide exogenous gene import in synthetic biology.Comment: Supporting information is available at PLoS Computational Biolog
Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation
Mutational analysis provides direct evidence for the link between proteorhodopsin light-harvesting and enhanced survival of marine bacteria
Function and Regulation of Vibrio campbellii Proteorhodopsin: Acquired Phototrophy in a Classical Organoheterotroph
Proteorhodopsins (PRs) are retinal-binding photoproteins that mediate light-driven proton translocation across prokaryotic cell membranes. Despite their abundance, wide distribution and contribution to the bioenergy budget of the marine photic zone, an understanding of PR function and physiological significance in situ has been hampered as the vast majority of PRs studied to date are from unculturable bacteria or culturable species that lack the tools for genetic manipulation. In this study, we describe the presence and function of a horizontally acquired PR and retinal biosynthesis gene cluster in the culturable and genetically tractable bioluminescent marine bacterium Vibrio campbellii. Pigmentation analysis, absorption spectroscopy and photoinduction assays using a heterologous over-expression system established the V. campbellii PR as a functional green light absorbing proton pump. In situ analyses comparing PR expression and function in wild type (WT) V. campbellii with an isogenic ΔpR deletion mutant revealed a marked absence of PR membrane localization, pigmentation and light-induced proton pumping in the ΔpR mutant. Comparative photoinduction assays demonstrated the distinct upregulation of pR expression in the presence of light and PR-mediated photophosphorylation in WT cells that resulted in the enhancement of cellular survival during respiratory stress. In addition, we demonstrate that the master regulator of adaptive stress response and stationary phase, RpoS1, positively regulates pR expression and PR holoprotein pigmentation. Taken together, the results demonstrate facultative phototrophy in a classical marine organoheterotrophic Vibrio species and provide a salient example of how this organism has exploited lateral gene transfer to further its adaptation to the photic zone
Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology
The biological world, especially its majority microbial component, is
strongly interacting and may be dominated by collective effects. In this
review, we provide a brief introduction for statistical physicists of the way
in which living cells communicate genetically through transferred genes, as
well as the ways in which they can reorganize their genomes in response to
environmental pressure. We discuss how genome evolution can be thought of as
related to the physical phenomenon of annealing, and describe the sense in
which genomes can be said to exhibit an analogue of information entropy. As a
direct application of these ideas, we analyze the variation with ocean depth of
transposons in marine microbial genomes, predicting trends that are consistent
with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic
Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics
BACKGROUND: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. METHODOLOGY/PRINCIPAL FINDINGS: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. CONCLUSIONS/SIGNIFICANCE: Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a "bramble" model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic "root". Structural diversification may be constrained ("trimmed") where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification
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