Molecular Mechanisms of CO2 Concentration and Proton Extrusion in Cyanobacteria

Global climate changes are imposing multiple pressures to marine organisms. The rising atmospheric CO2 concentration is causing substantial changes in ocean physics, chemistry and biology. At least three synergic environmental stressors have been recognized as primary driven by CO2 emissions: ocean warming, oxygen loss and ocean acidification. The effects of CO2-driven ocean acidification on seagrass metabolism remain largely understudied. A few studies have been conducted near submarine volcanic vents, which mimic the future ocean acidification scenarios, allowing researchers to investigate the performance of marine organisms under long-term exposure to high-CO2 levels. Apart from these, some mesocosm-based experiments have investigated growth and physiological responses to high CO2. For this work, we built an outdoor mesocosm facility at the Centre of Marine Sciences’ field station in Algarve, Portugal, to experimentally manipulate CO2 levels and investigate the effects of high-CO2/low pH on seagrass metabolism and underlying molecular mechanisms. Cymodocea nodosa plants were collected in Cadiz Bay at the end of January 2014 and transported to the mesocosm facility. After a one week acclimation period, C. nodosa were either kept under normal (400 ppm) or elevated (1200 ppm) CO2 concentration for 12 days. Water physico-chemical parameters, irradiance, and chlorophyll-fluorescence-derived photosynthetic parameters were monitored on a daily basis. Here we present, for the first time in this species, results obtained using Illumina RNAseq technology and de-novo transcriptome assembly. Using C. nodosa RNAs extracted at the beginning and the end of the experiment, we assembled more than 70 thousands unique transcripts and were able to annotate more than 90% of them using the Annocript pipeline. Differential expression analysis revealed about 500 transcripts significantly differentially regulated between plants kept under control and high-CO2 conditions. Pathways showing largest changes in gene expression included isoprenoid and amino-acid biosynthesis, porphyrin-containing compound metabolism, amine and polyamine biosynthesis, lipid and carbohydrate metabolism. Transcriptome sequencing also significantly increases the molecular resources available for C. nodosa, almost completely absent before this study.

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Cymodocea nodosa response to simulated CO2-driven ocean acidification: a first insight from global transcriptome profiling

10.7287/peerj.preprints.1057 ◽

2015 ◽

Author(s):

Miriam Ruocco ◽

Procaccini Gabriele ◽

Francesco Musacchia ◽

Remo Sanges ◽

Irene Olivé ◽

...

Keyword(s):

Ocean Acidification ◽

Molecular Mechanisms ◽

Transcriptome Assembly ◽

Co2 Concentration ◽

Marine Organisms ◽

Photosynthetic Parameters ◽

Cymodocea Nodosa ◽

Field Station ◽

High Co2 ◽

Co2 Levels

Global climate changes are imposing multiple pressures to marine organisms. The rising atmospheric CO2 concentration is causing substantial changes in ocean physics, chemistry and biology. At least three synergic environmental stressors have been recognized as primary driven by CO2 emissions: ocean warming, oxygen loss and ocean acidification. The effects of CO2-driven ocean acidification on seagrass metabolism remain largely understudied. A few studies have been conducted near submarine volcanic vents, which mimic the future ocean acidification scenarios, allowing researchers to investigate the performance of marine organisms under long-term exposure to high-CO2 levels. Apart from these, some mesocosm-based experiments have investigated growth and physiological responses to high CO2. For this work, we built an outdoor mesocosm facility at the Centre of Marine Sciences’ field station in Algarve, Portugal, to experimentally manipulate CO2 levels and investigate the effects of high-CO2/low pH on seagrass metabolism and underlying molecular mechanisms. Cymodocea nodosa plants were collected in Cadiz Bay at the end of January 2014 and transported to the mesocosm facility. After a one week acclimation period, C. nodosa were either kept under normal (400 ppm) or elevated (1200 ppm) CO2 concentration for 12 days. Water physico-chemical parameters, irradiance, and chlorophyll-fluorescence-derived photosynthetic parameters were monitored on a daily basis. Here we present, for the first time in this species, results obtained using Illumina RNAseq technology and de-novo transcriptome assembly. Using C. nodosa RNAs extracted at the beginning and the end of the experiment, we assembled more than 70 thousands unique transcripts and were able to annotate more than 90% of them using the Annocript pipeline. Differential expression analysis revealed about 500 transcripts significantly differentially regulated between plants kept under control and high-CO2 conditions. Pathways showing largest changes in gene expression included isoprenoid and amino-acid biosynthesis, porphyrin-containing compound metabolism, amine and polyamine biosynthesis, lipid and carbohydrate metabolism. Transcriptome sequencing also significantly increases the molecular resources available for C. nodosa, almost completely absent before this study.

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Transcription factor/DNA interactions visualized by electron spectroscopic imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100122654 ◽

1992 ◽

Vol 50 (1) ◽

pp. 450-451

Author(s):

David P. Bazett-Jones ◽

Mark L. Brown

Keyword(s):

Transcription Factor ◽

Dna Sequences ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Phosphorus Content ◽

Spectroscopic Imaging ◽

Electron Spectroscopic Imaging ◽

Dna Backbone ◽

Two Parameters ◽

High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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Dissection of the molecular mechanisms of protein targeting to the peroxisome using immunofluorescence and immunocryoelectron microscopies

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100157760 ◽

1990 ◽

Vol 48 (3) ◽

pp. 44-45

Author(s):

G-A. Keller ◽

S. J. Gould ◽

S. Subramani ◽

S. Krisans

Keyword(s):

Mammalian Cells ◽

Molecular Mechanisms ◽

Protein Targeting ◽

Firefly Luciferase ◽

Peroxisomal Enzyme ◽

Transfected Cells ◽

Peroxisomal Targeting ◽

Targeting Signal ◽

Series Of Experiments ◽

Peroxisomal Targeting Signal

Subcellular compartments within eukaryotic cells must each be supplied with unique sets of proteins that must be directed to, and translocated across one or more membranes of the target organelles. This transport is mediated by cis- acting targeting signals present within the imported proteins. The following is a chronological account of a series of experiments designed and carried out in an effort to understand how proteins are targeted to the peroxisomal compartment.-We demonstrated by immunocryoelectron microscopy that the enzyme luciferase is a peroxisomal enzyme in the firefly lantern. -We expressed the cDNA encoding firefly luciferase in mammalian cells and demonstrated by immunofluorescence that the enzyme was transported into the peroxisomes of the transfected cells. -Using deletions, linker insertions, and gene fusion to identify regions of luciferase involved in its transport to the peroxisomes, we demonstrated that luciferase contains a peroxisomal targeting signal (PTS) within its COOH-terminal twelve amino acid.

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High resolution mapping of nucleic acid containing complexes in vitro and in situ

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162703 ◽

1996 ◽

Vol 54 ◽

pp. 48-49

Author(s):

D. P. Bazett-Jones ◽

M. J. Hendzel

Keyword(s):

Nucleic Acid ◽

High Resolution ◽

Transcription Initiation ◽

Molecular Mechanisms ◽

Heavy Atom ◽

Regulation Of Transcription ◽

High Exposure ◽

Resolution Mapping ◽

Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

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How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

Biochemical Society Transactions ◽

10.1042/bst20190944 ◽

2020 ◽

Vol 48 (3) ◽

pp. 1019-1034 ◽

Cited By ~ 1

Author(s):

Rachel M. Woodhouse ◽

Alyson Ashe

Keyword(s):

Histone Modifications ◽

Molecular Mechanisms ◽

Epigenetic Inheritance ◽

Nematode Caenorhabditis Elegans ◽

Histone Methyltransferases ◽

Transgenerational Epigenetic Inheritance ◽

C Elegans ◽

Recent Developments ◽

Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

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Mesophyll conductance: the leaf corridors for photosynthesis

Biochemical Society Transactions ◽

10.1042/bst20190312 ◽

2020 ◽

Vol 48 (2) ◽

pp. 429-439 ◽

Cited By ~ 3

Author(s):

Jorge Gago ◽

Danilo M. Daloso ◽

Marc Carriquí ◽

Miquel Nadal ◽

Melanie Morales ◽

...

Keyword(s):

Molecular Mechanisms ◽

Current Knowledge ◽

Main Role ◽

Mesophyll Conductance ◽

Future Studies ◽

Cell Structures ◽

Leaf Tissues ◽

Change Framework ◽

Chloroplast Stroma

Besides stomata, the photosynthetic CO2 pathway also involves the transport of CO2 from the sub-stomatal air spaces inside to the carboxylation sites in the chloroplast stroma, where Rubisco is located. This pathway is far to be a simple and direct way, formed by series of consecutive barriers that the CO2 should cross to be finally assimilated in photosynthesis, known as the mesophyll conductance (gm). Therefore, the gm reflects the pathway through different air, water and biophysical barriers within the leaf tissues and cell structures. Currently, it is known that gm can impose the same level of limitation (or even higher depending of the conditions) to photosynthesis than the wider known stomata or biochemistry. In this mini-review, we are focused on each of the gm determinants to summarize the current knowledge on the mechanisms driving gm from anatomical to metabolic and biochemical perspectives. Special attention deserve the latest studies demonstrating the importance of the molecular mechanisms driving anatomical traits as cell wall and the chloroplast surface exposed to the mesophyll airspaces (Sc/S) that significantly constrain gm. However, even considering these recent discoveries, still is poorly understood the mechanisms about signaling pathways linking the environment a/biotic stressors with gm responses. Thus, considering the main role of gm as a major driver of the CO2 availability at the carboxylation sites, future studies into these aspects will help us to understand photosynthesis responses in a global change framework.

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Inflammageing in the cardiovascular system: mechanisms, emerging targets, and novel therapeutic strategies

Clinical Science ◽

10.1042/cs20191213 ◽

2020 ◽

Vol 134 (17) ◽

pp. 2243-2262

Author(s):

Danlin Liu ◽

Gavin Richardson ◽

Fehmi M. Benli ◽

Catherine Park ◽

João V. de Souza ◽

...

Keyword(s):

Cardiovascular Diseases ◽

Cardiovascular System ◽

Nlrp3 Inflammasome ◽

Molecular Mechanisms ◽

Molecular Targets ◽

Therapeutic Interventions ◽

Low Grade ◽

Cardiovascular Research ◽

Inflammatory Processes ◽

Ach Receptors

Abstract In the elderly population, pathological inflammation has been associated with ageing-associated diseases. The term ‘inflammageing’, which was used for the first time by Franceschi and co-workers in 2000, is associated with the chronic, low-grade, subclinical inflammatory processes coupled to biological ageing. The source of these inflammatory processes is debated. The senescence-associated secretory phenotype (SASP) has been proposed as the main origin of inflammageing. The SASP is characterised by the release of inflammatory cytokines, elevated activation of the NLRP3 inflammasome, altered regulation of acetylcholine (ACh) nicotinic receptors, and abnormal NAD+ metabolism. Therefore, SASP may be ‘druggable’ by small molecule therapeutics targeting those emerging molecular targets. It has been shown that inflammageing is a hallmark of various cardiovascular diseases, including atherosclerosis, hypertension, and adverse cardiac remodelling. Therefore, the pathomechanism involving SASP activation via the NLRP3 inflammasome; modulation of NLRP3 via α7 nicotinic ACh receptors; and modulation by senolytics targeting other proteins have gained a lot of interest within cardiovascular research and drug development communities. In this review, which offers a unique view from both clinical and preclinical target-based drug discovery perspectives, we have focused on cardiovascular inflammageing and its molecular mechanisms. We have outlined the mechanistic links between inflammageing, SASP, interleukin (IL)-1β, NLRP3 inflammasome, nicotinic ACh receptors, and molecular targets of senolytic drugs in the context of cardiovascular diseases. We have addressed the ‘druggability’ of NLRP3 and nicotinic α7 receptors by small molecules, as these proteins represent novel and exciting targets for therapeutic interventions targeting inflammageing in the cardiovascular system and beyond.

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