Physiology and molecular biology of aquatic cyanobacteria

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 359, doi:10.3389/fmicb.2014.00359.Cyanobacteria thrive in every illuminated aquatic environment known, contributing at least 25% of primary productivity worldwide. Given their importance in carbon and nutrient cycles, cyanobacteria are essential geochemical agents that have shaped the composition of the Earth's crust, oceans and atmosphere for billions of years. The high diversity of cyanobacteria is reflected in the panoply of unique physiological adaptations across the phylum, including different strategies to optimize light harvesting or sustain nitrogen fixation, but also different lifestyles like psychrotrophy, and oligotrophy. Some cyanobacteria produce secondary metabolites of cryptic function, many of which are toxic to eukaryotes. Consequently, bloom-forming toxic cyanobacteria are global hazards that are of increasing concern in surface waters affected by anthropogenic nutrient loads and climate change

Nmr Solution Structure Of Plastocyanin From The Photosynthetic Prokaryote, Prochlorothrix Hollandica

The solution structure of a divergent plastocyanin (PC) from the photosynthetic prokaryote Prochlorothrix hollandica was determined by homonuclear H-1 NMR spectroscopy. Nineteen structures were calculated from 1222 distance restraints, yielding a family of structures having an average rmsd of 0.42 +/- 0.08 Angstrom, for backbone atoms and 0.71 +/- 0.07 Angstrom for heavy atoms to the mean structure. No distance constraint was violated by more than 0.26 Angstrom in the structure family. Despite the low number of conserved residues shared with other PC homologues, the overall folding pattern of P. hollandica PC is similar to other PCs, in that the protein forms a two-sheet beta-barrel tertiary structure. The greatest variability among the backbone structures is seen in the loop region from residues 47-60. The differences seen in the P. hollandica PC homologue likely arise due to a small deletion of 2-4 residues compared to the PC consensus; this yields a less extended loop containing a short alpha-helix from residues Ala52-Leu55. Additionally, the protein has an altered hydrophobic patch thought to be important in binding reaction partners. Whereas the backbone structure is very similar within the loops of the hydrophobic region, the presence of two unique residues (Tyr12 and Pro14) yields a structurally different hydrophobic surface likely important in binding P. hollandica Photosystem I

Monomer dynamics of a wormlike chain

We derive the stochastic equations of motion for a tracer that is tightly attached to a semiflexible polymer and confined or agitated by an externally controlled potential. The generalised Langevin equation, the power spectrum, and the mean-square displacement for the tracer dynamics are explicitly constructed from the microscopic equations of motion for a weakly bending wormlike chain by a systematic coarse-graining procedure. Our accurate analytical expressions should provide a convenient starting point for further theoretical developments and for the analysis of various single-molecule experiments and of protein shape fluctuations.Comment: 6 pages, 4 figure

Identification, enumeration and diversity of nitrifying planktonic archaea and bacteria in trophic end members of the Laurentian Great Lakes

Oligotrophic Lake Superior and mesotrophic Lake Erie are trophic end members of the hydrologically connected Laurentian Great Lakes system, and as such exhibit different profiles of dissolved nitrogen species. Nitrification in Lake Superior has led to increasing nitrate concentrations over the past century, as opposed to Erie, where nitrate inventories have declined due to denitrification. In this study, we examined the abundance and diversity of nitrifying microbes involved in the oxidation of ammonia to nitrite, and nitrite to nitrate. By in situ hybridization methods, we enumerated the major planktonic ammonia oxidizing bacteria (AOB) and archaea (AOA) during a July 2011 cruise from Lake Superior to Lake Erie. In Lake Superior, AOA dominated compared to AOB, typically exceeding 5 × 103 mL-1, whereas in Erie, AOB were more abundant than AOA. These data parallel prior work on Lake Superior and Lake Erie sediments, in which AOA are far more abundant in Superior, but AOB dominate in Erie. The lakes were sampled during stratification, and AOA and AOB were largely restricted to the hypolimnion, consistent with the observation that ammonia oxidizers are photoinhibited in surface waters. In Lakes Superior and Erie, we also detected nitrite oxidizing bacteria (NOB) in a pattern paralleling AOA/AOB abundance. Phylogenetic analysis of archaeal 16S rRNA revealed that the planktonic archaea of Lake Superior are members of the ammonia oxidizing Group I.1a Thaumarchaeota most closely related to Nitrosoarchaeum limnia. These AOA are distinct from the Group I.1a AOA in Lake Superior sediments. The major AOB of Lake Erie form a subcluster within the genus Nitrosospira

Microcystin aids in cold temperature acclimation: Differences between a toxic Microcystis wildtype and non-toxic mutant

For Microcystis aeruginosa PCC 7806, temperature decreases from 26 °C to 19 °C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin provided M. aeruginosa PCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, reactive oxygen species damage, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strain M. aeruginosa PCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19 °C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e., making microcystin) vs the shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents

Sulfolipid substitution ratios of Microcystis aeruginosa and planktonic communities as an indicator of phosphorus limitation in Lake Erie

Phosphorus (P) availability frequently limits primary production in lakes, influences the physiology of phytoplankton, shapes community structure, and can stimulate or constrain the formation of cyanobacterial blooms. Given the importance of P, numerous methods are available to assess P stress in phytoplankton communities. Marine phytoplankton are known to substitute sulfolipids for phospholipids in response to P limitation. We asked whether sulfolipid substitution might serve as an additional indicator of P stress in freshwater phytoplankton communities. The question was addressed using cultures of Microcystis aeruginosa, Lake Erie microcosms, and surveys of lipid profiles in Lake Erie during a Microcystis spp. bloom. Peak area response ratios of the intact polar lipids sulfoquinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG) were used as the metric of lipid substitution. In cultures of M. aeruginosa NIES-843, the SQDG : PG ratio increased from ~ 0.9 to ~ 3.3 with decreasing P concentration. In P-limited communities, the SQDG : PG ratio increased from ~ 6 to ~ 11 after 48 h in microcosm controls, while P amendments reduced the ratio to ~ 3. In Lake Erie surveys, the SQDG : PG ratio ranged from ~ 0.4 to ~ 7.4 and was negatively correlated (Pearson r = −0.62) with total dissolved P. The SQDG : PG ratio was not correlated with concentrations of chlorophyll a, soluble reactive P, or N : P molar ratios. These results demonstrated that M. aeruginosa and Microcystis-dominated communities remodel lipid profiles in response to P scarcity, providing a potential short-term, time-integrated biomarker of nutrient history and P stress in fresh waters

Enthalpy of formation of ye’elimite and ternesite

Calcium sulfoaluminate clinkers containing ye’elimite (Ca4Al6O12(SO4)) and ternesite (Ca5(SiO4)2SO4) are being widely investigated as components of calcium sulfoaluminate cement clinkers. These may become low energy replacements for Portland cement. Conditional thermodynamic data for ye’elimite and ternesite (enthalpy of formation) have been determined experimentally using a combination of techniques: isothermal conduction calorimetry, X-ray powder diffraction and thermogravimetric analysis. The enthalpies of formation of ye’elimite and ternesite at 25 °C were determined to be − 8523 and − 5993 kJ mol−1, respectively

Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations

International audienceThe mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods matured thanks to the development of nanotechnologies such as optical and magnetic tweezers, the biomembrane force probe and atomic force microscopy (AFM). The quantitative nature of force spectroscopy measurements has converted AFM into a valuable tool in biophysics. Force spectroscopy allows the determination of the forces required to unfold protein domains and to disrupt individual receptor/ligand bonds. Molecular simulation as a computational microscope allows investigation of similar biological processes with an atomistic detail. In this chapter, we first provide a step-by-step protocol of force spectroscopy including sample preparation, measurement and analysis of force spectroscopy using AFM and its interpretation in terms of available theories. Next, we present the background for molecular dynamics (MD) simulations focusing on steered molecular dynamics (SMD) and the importance of bridging of computational tools with experimental technique

Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene

Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms.Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas.The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia

Hypothesis for the evolution of three-helix Chl a/b and Chl a/c light-harvesting antenna proteins from two-helix and four-helix ancestors

The nuclear-encoded Chl a/b and Chl a/c antenna proteins of photosynthetic eukaryotes are part of an extended family of proteins that also includes the early light-induced proteins (ELIPs) and the 22 kDa intrinsic protein of PS II (encoded by psb S gene). All members of this family have three transmembrane helices except for the psb S protein, which has four. The amino acid sequences of these proteins are compared and related to the three-dimensional structure of pea LHC II Type I (Kühlbrandt and Wang, Nature 350: 130–134, 1991). The similarity of psb S to the three-helix members of the family suggests that the latter arose from a four-helix ancestor that lost its C-terminal helix by deletion. Strong internal similarity between the two halves of the psb S protein suggests that it in turn arose as the result of the duplication of a gene encoding a two-helix protein. Since psb S is reported to be present in at least one cyanobacterium, the ancestral four-helix protein may have been present prior to the endosymbiotic event or events that gave rise to the photosynthetic eukaryotes. The Chl a/b and Chl a/c antenna proteins, and the immunologically-related proteins in the rhodophytes may have had a common ancestor which was present in the early photosynthetic eukaryotes, and predated their division into rhodophyte, chromophyte and chlorophyte lineages. The LHC I-LHC II divergence probably occurred before the separation of higher plants from chlorophyte algae and euglenophytes, and the different Types of LHC I and LHC II proteins arose prior to the separation of angiosperms and gymnosperms.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43538/1/11120_2004_Article_BF00029382.pd