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101. Additional file 1 of BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Author

Sutter, Markus and Kerfeld, Cheryl A.

Abstract

Additional file 1: Fig. S1. Overview of interface and result pages. a Landing page with brief introduction to BMC structure and function. b Submission form for locus type analysis and example result page of locus analysis. Bar length is scaled to gene length. c Example result page of shell protein analysis. Figure S2. Example output for a novel type of BMC. a BMC shell protein analysis of the whole proteome of this metagenome assembled genome (MAG) with id 3300010269_9. b BMC locus analysis of the region around the shell proteins from Ga0134102_1000278_11 to Ga0134102_1000278_29. c Close-up view of pores in the homology model structures predicted with SWISS-MODEL for the H_azure (based on pdb ID 3MPY) and H_fuchsia (based on pdb ID 4AXJ) The residues converging at the pores of the hexamers are shown in sticks.

Published
2022
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111. Structures of the Cyanobacterial Phycobilisome

Author

Sauer, Paul V., primary, Dominguez-Martin, Maria Agustina, additional, Kirst, Henning, additional, Sutter, Markus, additional, Bina, David, additional, Greber, Basil J., additional, Nogales, Eva, additional, Polívka, Tomáš, additional, and Kerfeld, Cheryl A., additional

Published
2021
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115. Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin

Author

Feroz, Hasin, primary, Ferlez, Bryan, additional, Oh, Hyeonji, additional, Mohammadiarani, Hossein, additional, Ren, Tingwei, additional, Baker, Carol S., additional, Gajewski, John P., additional, Lugar, Daniel J., additional, Gaudana, Sandeep B., additional, Butler, Peter, additional, Hühn, Jonas, additional, Lamping, Matthias, additional, Parak, Wolfgang J., additional, Blatt, Michael R., additional, Kerfeld, Cheryl A., additional, Smirnoff, Nicholas, additional, Vashisth, Harish, additional, Golbeck, John H., additional, and Kumar, Manish, additional

Published
2021
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117. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

128. Dynamic structural determinants in bacterial microcompartment shells.

Author

Trettel, Daniel S, Kerfeld, Cheryl A, and Gonzalez-Esquer, Cesar R

Subjects
*STRUCTURAL dynamics, *STRUCTURAL shells, *BIOTECHNOLOGY, *CARBON dioxide, *POLYHEDRA
Abstract

Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO 2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks. [Display omitted] • Bacterial microcompartments are self-assembling protein polyhedra composed of an outer shell and encapsulated inner cargo. • The proteins that form the shell use conserved assembly principles, predominately encoded by the Pfam00936 domain. • The plasticity of interactions has structural implications for size, overall morphology, and function of shell assemblies. • The structural plasticity of shell subunits can affect features like quaternary polymorphisms and ligand-mediated allostery. [ABSTRACT FROM AUTHOR]

Published
2024
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129. Structures of a phycobilisome in light-harvesting and photoprotected states

Author

Domínguez-Martín, María Agustina, Sauer, Paul V., Kirst, Henning, Sutter, Markus, Bína, David, Greber, Basil J., Nogales, Eva, Polívka, Tomáš, and Kerfeld, Cheryl A.

Abstract

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae1,2. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching3–6. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystissp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP–PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties7, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

Published
2022
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130. Atypical Carboxysome Loci: JEEPs or Junk?

Author

Sutter, Markus, Kerfeld, Cheryl A., and Scott, Kathleen M.

Subjects
LOCUS (Genetics), CARBONIC anhydrase, BIOLOGICAL transport, CARBON dioxide fixation, OPERONS, NUCLEOTIDE sequencing, OXYGENASES
Abstract

Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria , primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3− in the cytoplasm via active transport, HCO3− enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3− to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts. [ABSTRACT FROM AUTHOR]

Published
2022
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131. BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data.

Author

Sutter, Markus and Kerfeld, Cheryl A.

Subjects
*INTERNET servers, *STRUCTURAL shells, *AMINO acid sequence, *MARKOV processes, *STRUCTURAL models, *PROTEIN models
Abstract

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a "do-it yourself" analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism's metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples. [ABSTRACT FROM AUTHOR]

Published
2022
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133. Structures of cytochrome c-549 and cytochrome c (sub)6 from the cyanobacterium Arthrospira maxima

Author

Sawaya, Michael R., Krogmann, David W., Serag, Ahmed, Ho, Kwok Ki, Yeates, Todd O., and Kerfeld, Cheryl A.

Subjects
Biochemistry -- Research, Cyanobacteria -- Physiological aspects, Cytochrome c -- Physiological aspects, Proteins -- Physiological aspects, Biological sciences, Chemistry
Abstract

Research has been conducted on the cytochrome c-549 and cytochrome c (sub)6. The X-ray structures of these proteins isolated from cyanobacterium Arthrospira maxima have been investigated and the results indicate that their structures are similar.

Published
2001

136. Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP

Author

Dominguez-Martin, Maria Agustina, primary, Hammel, Michal, additional, Gupta, Sayan, additional, Lechno-Yossef, Sigal, additional, Sutter, Markus, additional, Rosenberg, Daniel J., additional, Chen, Yan, additional, Petzold, Christopher J., additional, Ralston, Corie Y., additional, Polívka, Tomáš, additional, and Kerfeld, Cheryl A., additional

Published
2020
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137. Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters

Author

Scott, Kathleen M, primary, Harmer, Tara L, additional, Gemmell, Bradford J, additional, Kramer, Andrew M, additional, Sutter, Markus, additional, Kerfeld, Cheryl A, additional, Barber, Kourtney S, additional, Bari, Saaurav, additional, Boling, Joshua W, additional, Campbell, Cassandra P, additional, Gallard-Gongora, Javier F, additional, Jackson, Jessica K, additional, Lobos, Aldo, additional, Mounger, Jeannie M, additional, Radulovic, Peter W, additional, Sanson, Jacqueline M, additional, Schmid, Sarah, additional, Takieddine, Candice, additional, Warlick, Kiley F, additional, and Whittaker, Robert, additional

Published
2020
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143. Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix

Author

Kuznetsova, Valentyna, primary, Dominguez-Martin, Maria Agustina, additional, Bao, Han, additional, Gupta, Sayan, additional, Sutter, Markus, additional, Kloz, Miroslav, additional, Rebarz, Mateusz, additional, Přeček, Martin, additional, Chen, Yan, additional, Petzold, Christopher J., additional, Ralston, Corie Y., additional, Kerfeld, Cheryl A., additional, and Polívka, Tomáš, additional

Published
2020
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146. Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate.

Author

Kirst, Henning, Ferlez, Bryan H., Lindner, Steffen N., Cotton, Charles A. R., Bar-Even, Arren, and Kerfeld, Cheryl A.

Subjects
SYNTHETIC enzymes, PYRUVATES, COENZYME A, ACETATES, AGRICULTURAL productivity
Abstract

Formate has great potential to function as a feedstock for biorefineries because it can be sustainably produced by a variety of processes that don’t compete with agricultural production. However, naturally formatotrophic organisms are unsuitable for large-scale cultivation, difficult to engineer, or have inefficient native formate assimilation pathways. Thus, metabolic engineering needs to be developed for model industrial organisms to enable efficient formatotrophic growth. Here, we build a prototype synthetic formate utilizing bacterial microcompartment (sFUT) encapsulating the oxygen-sensitive glycyl radical enzyme pyruvate formate lyase and a phosphate acyltransferase to convert formate and acetylphosphate into the central biosynthetic intermediate pyruvate. This metabolic module offers a defined environment with a private cofactor coenzyme A that can cycle efficiently between the encapsulated enzymes. To facilitate initial design-build-test-refine cycles to construct an active metabolic core, we used a “wiffleball” architecture, defined as an icosahedral bacterial microcompartment (BMC) shell with unoccupied pentameric vertices to freely permit substrate and product exchange. The resulting sFUT prototype wiffleball is an active multi enzyme synthetic BMC functioning as platform technology. [ABSTRACT FROM AUTHOR]

Published
2022
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147. UV Excitation of Carotenoid Binding Proteins OCP and HCP: Excited‐State Dynamics and Product Formation.

Author

Khan, Tuhin, Kuznetsova, Valentyna, Dominguez‐Martin, Maria Agustina, Kerfeld, Cheryl A., and Polívka, Tomáš

Subjects
CARRIER proteins, RADICAL cations, CAROTENOIDS, AMINO acids, TRYPTOPHAN, PROTEINS
Abstract

Over the last decade the orange carotenoid protein (OCP) gained attention due to its role in photoprotection in cyanobacteria. Recently, other carotenoid binding proteins such as helical carotenoid proteins (HCPs) have been identified and characterized, although the function of the HCPs is not yet clarified. Here we have examined OCP1 and two HCPs, HCP2 and HCP3, from Tolypothrix PCC 7601 by ultrafast spectroscopy after excitation of both carotenoid canthaxanthin and amino acids tryptophan and tyrosine in UV at 275 nm. We find that the canthaxanthin S1 lifetime remains the same 3.5 ps as for excitation of the carotenoid S2 state, but the S* signal is significantly amplified by UV excitation. In contrast to the S2 excitation, we observe a formation of the canthaxanthin radical cation at 900 nm for all three proteins after 275 nm excitation. In OCP1, UV light also enhances the amplitude of spectral band centered at 550 nm at longer delays. This band likely corresponds to the first photoproduct of the OCP photocycle, suggesting that excess energy excitation and/or direct excitation of amino acids can enhance the product formation. [ABSTRACT FROM AUTHOR]

Published
2022
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149. Ultrafast spectroscopy and structural analysis explain differences between the photoactivation mechanism of OCP1 and OCP2

Author

Kuznetsova, Valentyna, Dominguez-Martin, Maria Agustina, Bao, Han, Gupta, Sayan, Sutter, Markus, Kloz, Miroslav, Rebarz, Mateusz, Přeček, Martin, Chen, Yan, Petzold, Christopher J., Ralston, Corie Y., Kerfeld, Cheryl A., and Polívka, Tomáš

Subjects
Spectrometry, Fluorescence, Bacterial Proteins, Phycobilisomes, Cyanobacteria, Article
Abstract

The orange carotenoid protein (OCP) is a structurally and functionally modular photoactive protein involved in cyanobacterial photoprotection. Recently, based on bioinformatic analysis and phylogenetic relationships, new families of OCP have been described, OCP2 and OCPx. The first characterization of the OCP2 showed both faster photoconversion and back-conversion, and lower fluorescence quenching of phycobilisomes relative to the well-characterized OCP1. Moreover, OCP2 is not regulated by the fluorescence recovery protein (FRP). In this work, we present a comprehensive study combining ultrafast spectroscopy and structural analysis to compare the photoactivation mechanisms of OCP1 and OCP2 from Tolypothrix PCC 7601. We show that despite significant differences in their functional characteristics, the spectroscopic properties of OCP1 and OCP2 are comparable. This indicates that the OCP functionality is not directly related to the spectroscopic properties of the bound carotenoid. In addition, the structural analysis by X-ray footprinting reveals that, overall, OCP1 and OCP2 have grossly the same photoactivation mechanism. However, the OCP2 is less reactive to radiolytic labeling, suggesting that the protein is less flexible than OCP1. This observation could explain fast photoconversion of OCP2.

Published
2019

150. Crystal structure and possible dimerization of the high-potential iron-sulfur protein from Chromatium purpuratum

Author

Kerfeld, Cheryl A., Salmeen, Annette E., and Yeates Todd O.

Subjects
Proteins -- Structure, Bacterial proteins -- Research, Metalloproteins -- Research, Biological sciences, Chemistry
Abstract

Biochemical characterization, crystallization and structure determination studies were undertaken to determine the crystal structure of the high-potential iron-sulfur protein from Chromatium purpuratum. The crystal structure was determined with a resolution of 2.7 angstrom units. The protein appears to undergo dimerization via nonspecific interactions at a conserved hydrophobic domain.

Published
1998

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