High-Value Recombinant Protein Production in Microalgae
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A Spatial Interactome Reveals the Protein Organization of the Algal
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Cell. Author Manuscript Author manuscript; Manuscript Author available in PMC 2018 September 21. Published in final edited form as: Cell. 2017 September 21; 171(1): 133–147.e14. doi:10.1016/j.cell.2017.08.044. A Spatial Interactome Reveals the Protein Organization of the Algal CO2 Concentrating Mechanism Luke C.M. Mackinder1,2, Chris Chen1,3, Ryan D. Leib4, Weronika Patena1, Sean R. Blum5, Matthew Rodman3, Silvia Ramundo6, Christopher M. Adams4, and Martin C. Jonikas1,3,7,8,* 1Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA 3Department of Biology, Stanford University, Stanford, CA 94305, USA 4Stanford University Mass Spectrometry, Stanford University, Stanford, CA, USA 5Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA 95064, USA 6Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA 7Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA SUMMARY Approximately one-third of global CO2 fixation is performed by eukaryotic algae. Nearly all algae enhance their carbon assimilation by operating a CO2-concentrating mechanism (CCM) built around an organelle called the pyrenoid, whose protein composition is largely unknown. Here, we developed tools in the model alga Chlamydomonas reinhardtii to determine the localizations of 135 candidate CCM proteins, and physical interactors of 38 of these proteins. Our data reveal the identity of 89 pyrenoid proteins, including Rubisco-interacting proteins, photosystem I assembly factor candidates and inorganic carbon flux components. We identify three previously un- described protein layers of the pyrenoid: a plate-like layer, a mesh layer and a punctate layer. -
Evaluation of Total Protein Production by Soil Cyanobacteria in Culture Filtrate at Various Incubations Periods
www.ijapbc.com IJAPBC – Vol. 5(3), Jul - Sep, 2016 ISSN: 2277 - 4688 INTERNATIONAL JOURNAL OF ADVANCES IN PHARMACY, BIOLOGY AND CHEMISTRY Research Article Evaluation of Total Protein Production by soil Cyanobacteria in culture filtrate at various Incubations periods Farida P. Minocheherhomji* and Aarti Pradhan *Department of Microbiology, B. P. Baria Science Institute, Navsari, Gujarat, India - 396445. ABSTRACT Cyanobacteria, also known as blue-green algae, are microscopic organisms that obtain their energy through photosynthesis, and are found in common and naturally occurring ecosystem sites like moist soil and water bodies. Cyanobacteria are in a range of shapes and sizes and can occur as single cells while others assemble into groups as colonies or filaments. Blue green algae produces many metabolites including amino acids, proteins, vitamins and plant growth regulators like auxins, gibberellins and abscisic acids. The present study has been undertaken to estimate the total protein in their culture filtrate during different incubation times using BG-11 broth and Pringsheim’s broth. Protein was estimated from culture filtrate by standard protocols. The present study revealed that the amount of biomass, protein and IAA by different Cyanobacterial species were increased with the corresponding incubation time, and showed maximum concentration of 24 μg/ml, 14 μg/ml and 32.5 μg/ml in Pringsheim’s broth after 30 days respectively. Key Words: Cyanobacteria, Nitrogen fixation and Protein production INTRODUCTION Cyanobacteria belong to the group of organisms repertoire of metabolic activities. They proliferate in called prokaryotes, which also includes bacteria, and diverse types of ecosystems - ranging from the cold can be regarded as simple in terms of their cell Tundra to the hot deserts, from surface waters of structure. -
The Plankton Lifeform Extraction Tool: a Digital Tool to Increase The
Discussions https://doi.org/10.5194/essd-2021-171 Earth System Preprint. Discussion started: 21 July 2021 Science c Author(s) 2021. CC BY 4.0 License. Open Access Open Data The Plankton Lifeform Extraction Tool: A digital tool to increase the discoverability and usability of plankton time-series data Clare Ostle1*, Kevin Paxman1, Carolyn A. Graves2, Mathew Arnold1, Felipe Artigas3, Angus Atkinson4, Anaïs Aubert5, Malcolm Baptie6, Beth Bear7, Jacob Bedford8, Michael Best9, Eileen 5 Bresnan10, Rachel Brittain1, Derek Broughton1, Alexandre Budria5,11, Kathryn Cook12, Michelle Devlin7, George Graham1, Nick Halliday1, Pierre Hélaouët1, Marie Johansen13, David G. Johns1, Dan Lear1, Margarita Machairopoulou10, April McKinney14, Adam Mellor14, Alex Milligan7, Sophie Pitois7, Isabelle Rombouts5, Cordula Scherer15, Paul Tett16, Claire Widdicombe4, and Abigail McQuatters-Gollop8 1 10 The Marine Biological Association (MBA), The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK. 2 Centre for Environment Fisheries and Aquacu∑lture Science (Cefas), Weymouth, UK. 3 Université du Littoral Côte d’Opale, Université de Lille, CNRS UMR 8187 LOG, Laboratoire d’Océanologie et de Géosciences, Wimereux, France. 4 Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK. 5 15 Muséum National d’Histoire Naturelle (MNHN), CRESCO, 38 UMS Patrinat, Dinard, France. 6 Scottish Environment Protection Agency, Angus Smith Building, Maxim 6, Parklands Avenue, Eurocentral, Holytown, North Lanarkshire ML1 4WQ, UK. 7 Centre for Environment Fisheries and Aquaculture Science (Cefas), Lowestoft, UK. 8 Marine Conservation Research Group, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK. 9 20 The Environment Agency, Kingfisher House, Goldhay Way, Peterborough, PE4 6HL, UK. 10 Marine Scotland Science, Marine Laboratory, 375 Victoria Road, Aberdeen, AB11 9DB, UK. -
Structure and Function of the Archaeal Response Regulator Chey
Structure and function of the archaeal response PNAS PLUS regulator CheY Tessa E. F. Quaxa, Florian Altegoerb, Fernando Rossia, Zhengqun Lia, Marta Rodriguez-Francoc, Florian Krausd, Gert Bangeb,1, and Sonja-Verena Albersa,1 aMolecular Biology of Archaea, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; bLandes-Offensive zur Entwicklung Wissenschaftlich- ökonomischer Exzellenz Center for Synthetic Microbiology & Faculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany; cCell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; and dFaculty of Chemistry, Philipps-University-Marburg, 35043 Marburg, Germany Edited by Norman R. Pace, University of Colorado at Boulder, Boulder, CO, and approved December 13, 2017 (received for review October 2, 2017) Motility is a central feature of many microorganisms and provides display different swimming mechanisms. Counterclockwise ro- an efficient strategy to respond to environmental changes. Bacteria tation results in smooth swimming in well-characterized peritri- and archaea have developed fundamentally different rotary motors chously flagellated bacteria such as Escherichia coli, whereas enabling their motility, termed flagellum and archaellum, respec- rotation in the opposite direction results in tumbling. In contrast, tively. Bacterial motility along chemical gradients, called chemo- in other bacteria (i.e., Vibrio alginolyticus) and haloarchaea, taxis, critically relies on the response regulator CheY, which, when clockwise rotation results -
Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes
G C A T T A C G G C A T genes Article Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes Yuxin Hu 1,2, Weiyue Xing 1,2, Zhengyu Hu 3 and Guoxiang Liu 1,* 1 Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; [email protected] (Y.H.); [email protected] (W.X.) 2 School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China 3 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; [email protected] * Correspondence: [email protected]; Tel.: +86-027-6878-0576 Received: 11 December 2019; Accepted: 15 January 2020; Published: 20 January 2020 Abstract: We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. Wefound phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. -
The Minor Transitions in Hierarchical Evolution and the Question of a Directional Bias
The minor transitions in hierarchical evolution and the question of a directional bias D. W. McSHEA Department of Biology, Duke University, Durham, NC 27708-0338, USA Keywords: Abstract complexity; The history of life shows a clear trend in hierarchical organization, revealed by evolutionary trends; the successive emergence of organisms with ever greater numbers of levels of hierarchy; nestedness and greater development, or `individuation', of the highest level. major transitions. Various arguments have been offered which suggest that the trend is the result of a directional bias, or tendency, meaning that hierarchical increases are more probable than decreases among lineages, perhaps because hierarchical increases are favoured, on average, by natural selection. Further, what little evidence exists seems to point to a bias: some major increases are known ± including the origin of the eukaryotic cell from prokaryotic cells and of animals, fungi and land plants from solitary eukaryotic cells ± but no major decreases (except in parasitic and commensal organisms), at least at the cellular and multicellular levels. The fact of a trend, combined with the arguments and evidence, might make a bias seem beyond doubt, but here I argue that its existence is an open empirical question. Further, I show how testing is possible. Maynard Smith & SzathmaÂry, 1995, 1999; SzathmaÂry & Introduction Maynard Smith, 1995; McShea, 1996a; Pettersson, 1996; One of the most salient and certain trends in the history Heylighen, 1999; Stewart, 2000; Wright, 2000; Knoll & of life is the increase in hierarchical structure in organ- Bambach, 2000). It is also ± to my knowledge ± isms. Figure 1 shows the approximate trajectory of the unchallenged. -
Depth-Stratified Functional and Taxonomic Niche Specialization in the ‘Core’ and ‘Flexible’ Pacific Ocean Virome
The ISME Journal (2015) 9, 472–484 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome Bonnie L Hurwitz1, Jennifer R Brum and Matthew B Sullivan Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large- scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (o5% of PCs) and revealed depth- related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth- related patterns in nature. -
The Symbiotic Green Algae, Oophila (Chlamydomonadales
University of Connecticut OpenCommons@UConn Master's Theses University of Connecticut Graduate School 12-16-2016 The yS mbiotic Green Algae, Oophila (Chlamydomonadales, Chlorophyceae): A Heterotrophic Growth Study and Taxonomic History Nikolaus Schultz University of Connecticut - Storrs, [email protected] Recommended Citation Schultz, Nikolaus, "The yS mbiotic Green Algae, Oophila (Chlamydomonadales, Chlorophyceae): A Heterotrophic Growth Study and Taxonomic History" (2016). Master's Theses. 1035. https://opencommons.uconn.edu/gs_theses/1035 This work is brought to you for free and open access by the University of Connecticut Graduate School at OpenCommons@UConn. It has been accepted for inclusion in Master's Theses by an authorized administrator of OpenCommons@UConn. For more information, please contact [email protected]. The Symbiotic Green Algae, Oophila (Chlamydomonadales, Chlorophyceae): A Heterotrophic Growth Study and Taxonomic History Nikolaus Eduard Schultz B.A., Trinity College, 2014 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science at the University of Connecticut 2016 Copyright by Nikolaus Eduard Schultz 2016 ii ACKNOWLEDGEMENTS This thesis was made possible through the guidance, teachings and support of numerous individuals in my life. First and foremost, Louise Lewis deserves recognition for her tremendous efforts in making this work possible. She has performed pioneering work on this algal system and is one of the preeminent phycologists of our time. She has spent hundreds of hours of her time mentoring and teaching me invaluable skills. For this and so much more, I am very appreciative and humbled to have worked with her. Thank you Louise! To my committee members, Kurt Schwenk and David Wagner, thank you for your mentorship and guidance. -
Cell Structure and Function in the Bacteria and Archaea
4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth. -
The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. -
Phylogenetic Analysis of ''Volvocacae'
Phylogenetic analysis of ‘‘Volvocacae’’ for comparative genetic studies Annette W. Coleman† Division of Biology and Medicine, Brown University, Providence, RI 02912 Edited by Elisabeth Gantt, University of Maryland, College Park, MD, and approved September 28, 1999 (received for review June 30, 1999) Sequence analysis based on multiple isolates representing essen- most of those obtained previously with data for other DNA tially all genera and species of the classic family Volvocaeae has regions in identifying major clades and their relationships. clarified their phylogenetic relationships. Cloned internal tran- However, the expanded taxonomic coverage revealed additional scribed spacer sequences (ITS-1 and ITS-2, flanking the 5.8S gene of and unexpected relationships. the nuclear ribosomal gene cistrons) were aligned, guided by ITS transcript secondary structural features, and subjected to parsi- Materials and Methods mony and neighbor joining distance analysis. Results confirm the The algal isolates that form the basis of this study are listed below notion of a single common ancestor, and Chlamydomonas rein- and Volvocacean taxonomy is summarized in Table 1. The taxon harditii alone among all sequenced green unicells is most similar. names are those found in the culture collection listings. Included Interbreeding isolates were nearest neighbors on the evolutionary is the Culture Collection designation [University of Texas, tree in all cases. Some taxa, at whatever level, prove to be clades National Institute for Environmental Studies (Japan), A.W.C. or by sequence comparisons, but others provide striking exceptions. R. C. Starr collection], an abbreviated name, and the GenBank The morphological species Pandorina morum, known to be wide- accession number. -
Fe-S Protein Synthesis in Green Algae Mitochondria
plants Review Fe-S Protein Synthesis in Green Algae Mitochondria Diego F. Gomez-Casati * , Maria V. Busi *, Julieta Barchiesi, Maria A. Pagani , Noelia S. Marchetti-Acosta and Agustina Terenzi Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, 2000 Rosario, Argentina; [email protected] (J.B.); [email protected] (M.A.P.); [email protected] (N.S.M.-A.); [email protected] (A.T.) * Correspondence: [email protected] (D.F.G.-C.); [email protected] (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.) Abstract: Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways.