1
|
Pulsford SB, Nguyen ND, Long BM. The ties that bind. Disordered linkers underpin carboxysome construction. Proc Natl Acad Sci U S A 2023; 120:e2316828120. [PMID: 37889932 PMCID: PMC10636299 DOI: 10.1073/pnas.2316828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Affiliation(s)
- Sacha B. Pulsford
- Research School of Chemistry, Australian National University, Acton, ACT2601, Australia
| | - Nghiem D. Nguyen
- Plant Science Division, Research School of Biology, Australian National University, Acton, ACT2601, Australia
| | - Benedict M. Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW2308, Australia
| |
Collapse
|
2
|
Nguyen ND, Pulsford SB, Hee WY, Rae BD, Rourke LM, Price GD, Long BM. Towards engineering a hybrid carboxysome. PHOTOSYNTHESIS RESEARCH 2023; 156:265-277. [PMID: 36892800 PMCID: PMC10154267 DOI: 10.1007/s11120-023-01009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments, whose structural features enable the encapsulated Rubisco holoenzyme to operate in a high-CO2 environment. Consequently, Rubiscos housed within these compartments possess higher catalytic turnover rates relative to their plant counterparts. This particular enzymatic property has made the carboxysome, along with associated transporters, an attractive prospect to incorporate into plant chloroplasts to increase future crop yields. To date, two carboxysome types have been characterized, the α-type that has fewer shell components and the β-type that houses a faster Rubisco. While research is underway to construct a native carboxysome in planta, work investigating the internal arrangement of carboxysomes has identified conserved Rubisco amino acid residues between the two carboxysome types which could be engineered to produce a new, hybrid carboxysome. In theory, this hybrid carboxysome would benefit from the simpler α-carboxysome shell architecture while simultaneously exploiting the higher Rubisco turnover rates in β-carboxysomes. Here, we demonstrate in an Escherichia coli expression system, that the Thermosynechococcus elongatus Form IB Rubisco can be imperfectly incorporated into simplified Cyanobium α-carboxysome-like structures. While encapsulation of non-native cargo can be achieved, T. elongatus Form IB Rubisco does not interact with the Cyanobium carbonic anhydrase, a core requirement for proper carboxysome functionality. Together, these results suggest a way forward to hybrid carboxysome formation.
Collapse
Affiliation(s)
- Nghiem Dinh Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sacha B Pulsford
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, The Australian National University, Building 46, Sullivan's Creek Road, Acton, ACT, 2601, Australia
| | - Wei Yi Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Loraine M Rourke
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia.
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Benedict M Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| |
Collapse
|
3
|
Tobolovskaya Y, Medvedev JJ, Medvedeva XV, Mesbahuddin MS, Rodriguez NEN, Kalyaanamoorthy S, Klinkova A. The bovine carbonic anhydrase promoted dehydration of bicarbonate to CO2 for the electrochemical production of syngas. J CO2 UTIL 2023. [DOI: 10.1016/j.jcou.2023.102461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
|
4
|
Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
Collapse
|
5
|
Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
Collapse
Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| |
Collapse
|
6
|
Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
Collapse
Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| |
Collapse
|
7
|
Minagawa J, Dann M. Extracellular CahB1 from Sodalinema gerasimenkoae IPPAS B-353 Acts as a Functional Carboxysomal β-Carbonic Anhydrase in Synechocystis sp. PCC6803. PLANTS (BASEL, SWITZERLAND) 2023; 12:265. [PMID: 36678979 PMCID: PMC9865033 DOI: 10.3390/plants12020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Cyanobacteria mostly rely on the active uptake of hydrated CO2 (i.e., bicarbonate ions) from the surrounding media to fuel their inorganic carbon assimilation. The dehydration of bicarbonate in close vicinity of RuBisCO is achieved through the activity of carboxysomal carbonic anhydrase (CA) enzymes. Simultaneously, many cyanobacterial genomes encode extracellular α- and β-class CAs (EcaA, EcaB) whose exact physiological role remains largely unknown. To date, the CahB1 enzyme of Sodalinema gerasimenkoae (formerly Microcoleus/Coleofasciculus chthonoplastes) remains the sole described active extracellular β-CA in cyanobacteria, but its molecular features strongly suggest it to be a carboxysomal rather than a secreted protein. Upon expression of CahB1 in Synechocystis sp. PCC6803, we found that its expression complemented the loss of endogenous CcaA. Moreover, CahB1 was found to localize to a carboxysome-harboring and CA-active cell fraction. Our data suggest that CahB1 retains all crucial properties of a cellular carboxysomal CA and that the secretion mechanism and/or the machinations of the Sodalinema gerasimenkoae carboxysome are different from those of Synechocystis.
Collapse
Affiliation(s)
- Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
| | - Marcel Dann
- Division of Environmental Photobiology, National Institute for Basic Biology (NIBB), Aichi, Okazaki 444-8585, Japan
- Plant Molecular Biology, Ludwig-Maximilian University (LMU) Munich, 82152 Planegg, Germany
| |
Collapse
|
8
|
Tang J, Zhou H, Yao D, Riaz S, You D, Klepacz-Smółka A, Daroch M. Comparative Genomic Analysis Revealed Distinct Molecular Components and Organization of CO 2-Concentrating Mechanism in Thermophilic Cyanobacteria. Front Microbiol 2022; 13:876272. [PMID: 35602029 PMCID: PMC9120777 DOI: 10.3389/fmicb.2022.876272] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 12/30/2022] Open
Abstract
Cyanobacteria evolved an inorganic carbon-concentrating mechanism (CCM) to perform effective oxygenic photosynthesis and prevent photorespiratory carbon losses. This process facilitates the acclimation of cyanobacteria to various habitats, particularly in CO2-limited environments. To date, there is limited information on the CCM of thermophilic cyanobacteria whose habitats limit the solubility of inorganic carbon. Here, genome-based approaches were used to identify the molecular components of CCM in 17 well-described thermophilic cyanobacteria. These cyanobacteria were from the genus Leptodesmis, Leptolyngbya, Leptothermofonsia, Thermoleptolyngbya, Thermostichus, and Thermosynechococcus. All the strains belong to β-cyanobacteria based on their β-carboxysome shell proteins with 1B form of Rubisco. The diversity in the Ci uptake systems and carboxysome composition of these thermophiles were analyzed based on their genomic information. For Ci uptake systems, two CO2 uptake systems (NDH-13 and NDH-14) and BicA for HCO3– transport were present in all the thermophilic cyanobacteria, while most strains did not have the Na+/HCO3– Sbt symporter and HCO3– transporter BCT1 were absent in four strains. As for carboxysome, the β-carboxysomal shell protein, ccmK2, was absent only in Thermoleptolyngbya strains, whereas ccmK3/K4 were absent in all Thermostichus and Thermosynechococcus strains. Besides, all Thermostichus and Thermosynechococcus strains lacked carboxysomal β-CA, ccaA, the carbonic anhydrase activity of which may be replaced by ccmM proteins as indicated by comparative domain analysis. The genomic distribution of CCM-related genes was different among the thermophiles, suggesting probably distinct expression regulation. Overall, the comparative genomic analysis revealed distinct molecular components and organization of CCM in thermophilic cyanobacteria. These findings provided insights into the CCM components of thermophilic cyanobacteria and fundamental knowledge for further research regarding photosynthetic improvement and biomass yield of thermophilic cyanobacteria with biotechnological potentials.
Collapse
Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Dan Yao
- School of Food and Bioengineering, Chengdu University, Chengdu, China
| | - Sadaf Riaz
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Anna Klepacz-Smółka
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Łódź University of Technology, Łódź, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| |
Collapse
|
9
|
Sutter M, Kerfeld CA, Scott KM. Atypical Carboxysome Loci: JEEPs or Junk? Front Microbiol 2022; 13:872708. [PMID: 35668770 PMCID: PMC9164163 DOI: 10.3389/fmicb.2022.872708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
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.
Collapse
Affiliation(s)
| | | | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, FL, United States
| |
Collapse
|
10
|
Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
Collapse
|
11
|
Sun H, Cui N, Han SJ, Chen ZP, Xia LY, Chen Y, Jiang YL, Zhou CZ. Complex structure reveals CcmM and CcmN form a heterotrimeric adaptor in β-carboxysome. Protein Sci 2021; 30:1566-1576. [PMID: 33928692 DOI: 10.1002/pro.4090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Carboxysome is an icosahedral self-assembled microcompartment that sequesters RuBisCO and carbonic anhydrases within a selectively permeable protein shell. The scaffolding proteins, CcmM, and CcmN were proposed to act as adaptors that crosslink the enzymatic core to shell facets. However, the details of interaction pattern remain unknown. Here we obtained a stable heterotrimeric complex of CcmM γ-carbonic anhydrase domain (termed CcmMNT ) and CcmN, with a 1:2 stoichiometry, which interacts with the shell proteins CcmO and CcmL in vitro. The 2.9 Å crystal structure of this heterotrimer revealed an asymmetric bundle composed of one CcmMNT and two CcmN subunits, all of which adopt a triangular left-handed β-helical barrel structure. The central CcmN subunit packs against CcmMNT and another CcmN subunit via a wall-to-edge or wall-to-wall pattern, respectively. Together with previous findings, we propose CcmMNT -CcmN functions as an adaptor to facilitate the recruitment of shell proteins and the assembly of intact β-carboxysome.
Collapse
Affiliation(s)
- Hui Sun
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ning Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shu-Jing Han
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ling-Yun Xia
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| |
Collapse
|
12
|
Rubisco proton production can drive the elevation of CO 2 within condensates and carboxysomes. Proc Natl Acad Sci U S A 2021; 118:2014406118. [PMID: 33931502 PMCID: PMC8106323 DOI: 10.1073/pnas.2014406118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Membraneless organelles containing the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO2 concentrating mechanisms to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO2 fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO2 within the organelle via a colocalized carbonic anhydrase (CA) and inwardly diffusing HCO3 -, which have accumulated in the cytoplasm via dedicated transporters. Here, we present a concept in which we consider the net of two protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction-diffusion compartment model to investigate functional advantages these protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO3 - accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived protons to drive the conversion of HCO3 - to CO2 via colocalized CA, enhancing both condensate [CO2] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (phosphoglycerate) plays an important role in modulating internal pH and CO2 generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO3 - accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO2 and low light environments.
Collapse
|
13
|
Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis. Nat Struct Mol Biol 2021; 28:909-922. [PMID: 34759380 PMCID: PMC8580825 DOI: 10.1038/s41594-021-00676-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/28/2021] [Indexed: 12/01/2022]
Abstract
Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
Collapse
|
14
|
Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Nat Commun 2020; 11:5195. [PMID: 33060577 PMCID: PMC7567890 DOI: 10.1038/s41467-020-18814-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 09/09/2020] [Indexed: 02/01/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole PD module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the PP to the PD module.
Collapse
|
15
|
Rohnke BA, Rodríguez Pérez KJ, Montgomery BL. Linking the Dynamic Response of the Carbon Dioxide-Concentrating Mechanism to Carbon Assimilation Behavior in Fremyella diplosiphon. mBio 2020; 11:e01052-20. [PMID: 32457252 PMCID: PMC7251215 DOI: 10.1128/mbio.01052-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria use a carbon dioxide (CO2)-concentrating mechanism (CCM) that enhances their carbon fixation efficiency and is regulated by many environmental factors that impact photosynthesis, including carbon availability, light levels, and nutrient access. Efforts to connect the regulation of the CCM by these factors to functional effects on carbon assimilation rates have been complicated by the aqueous nature of cyanobacteria. Here, we describe the use of cyanobacteria in a semiwet state on glass fiber filtration discs-cyanobacterial discs-to establish dynamic carbon assimilation behavior using gas exchange analysis. In combination with quantitative PCR (qPCR) and transmission electron microscopy (TEM) analyses, we linked the regulation of CCM components to corresponding carbon assimilation behavior in the freshwater, filamentous cyanobacterium Fremyella diplosiphon Inorganic carbon (Ci) levels, light quantity, and light quality have all been shown to influence carbon assimilation behavior in F. diplosiphon Our results suggest a biphasic model of cyanobacterial carbon fixation. While behavior at low levels of CO2 is driven mainly by the Ci uptake ability of the cyanobacterium, at higher CO2 levels, carbon assimilation behavior is multifaceted and depends on Ci availability, carboxysome morphology, linear electron flow, and cell shape. Carbon response curves (CRCs) generated via gas exchange analysis enable rapid examination of CO2 assimilation behavior in cyanobacteria and can be used for cells grown under distinct conditions to provide insight into how CO2 assimilation correlates with the regulation of critical cellular functions, such as the environmental control of the CCM and downstream photosynthetic capacity.IMPORTANCE Environmental regulation of photosynthesis in cyanobacteria enhances organismal fitness, light capture, and associated carbon fixation under dynamic conditions. Concentration of carbon dioxide (CO2) near the carbon-fixing enzyme RubisCO occurs via the CO2-concentrating mechanism (CCM). The CCM is also tuned in response to carbon availability, light quality or levels, or nutrient access-cues that also impact photosynthesis. We adapted dynamic gas exchange methods generally used with plants to investigate environmental regulation of the CCM and carbon fixation capacity using glass fiber-filtered cells of the cyanobacterium Fremyella diplosiphon We describe a breakthrough in measuring real-time carbon uptake and associated assimilation capacity for cells grown in distinct conditions (i.e., light quality, light quantity, or carbon status). These measurements demonstrate that the CCM modulates carbon uptake and assimilation under low-Ci conditions and that light-dependent regulation of pigmentation, cell shape, and downstream stages of carbon fixation are critical for tuning carbon uptake and assimilation.
Collapse
Affiliation(s)
- Brandon A Rohnke
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Kiara J Rodríguez Pérez
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- University of Puerto Rico at Arecibo, Arecibo, Puerto Rico
| | - Beronda L Montgomery
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
16
|
Rohnke BA, Kerfeld CA, Montgomery BL. Binding Options for the Small Subunit-Like Domain of Cyanobacteria to Rubisco. Front Microbiol 2020; 11:187. [PMID: 32180764 PMCID: PMC7059596 DOI: 10.3389/fmicb.2020.00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
Two proteins found in cyanobacteria contain a C-terminal domain with homology to the small subunit of rubisco (RbcS). These small subunit-like domains (SSLDs) are important features of CcmM, a protein involved in the biogenesis of carboxysomes found in all β-cyanobacteria, and a rubisco activase homolog [activase-like protein of cyanobacteria (ALC)] found in over a third of sequenced cyanobacterial genomes. Interaction with rubisco is crucial to the function of CcmM and is believed to be important to ALC as well. In both cases, the SSLD aggregates rubisco, and this nucleation event may be important in regulating rubisco assembly and activity. Recently, two independent studies supported the conclusion that the SSLD of CcmM binds equatorially to L8S8 holoenzymes of rubisco rather than by displacing an RbcS, as its structural homology would suggest. We use sequence analysis and homology modeling to examine whether the SSLD from the ALC could bind the large subunit of rubisco either via an equatorial interaction or in an RbcS site, if available. We suggest that the SSLD from the ALC of Fremyella diplosiphon could bind either in a vacant RbcS site or equatorially. Our homology modeling takes into account N-terminal residues not represented in available cryo-electron microscopy structures that potentially contribute to the interface between the large subunit of rubisco (RbcL) and RbcS. Here, we suggest the perspective that binding site variability as a means of regulation is plausible and that the dynamic interaction between the RbcL, RbcS, and SSLDs may be important for carboxysome assembly and function.
Collapse
Affiliation(s)
- Brandon A Rohnke
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.,Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
17
|
Kalnins G, Cesle EE, Jansons J, Liepins J, Filimonenko A, Tars K. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nat Commun 2020; 11:388. [PMID: 31959751 PMCID: PMC6971018 DOI: 10.1038/s41467-019-14205-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/18/2019] [Indexed: 11/08/2022] Open
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
Collapse
Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia.
| | - Eva-Emilija Cesle
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Anatolij Filimonenko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| |
Collapse
|
18
|
Lechno-Yossef S, Rohnke BA, Belza ACO, Melnicki MR, Montgomery BL, Kerfeld CA. Cyanobacterial carboxysomes contain an unique rubisco-activase-like protein. THE NEW PHYTOLOGIST 2020; 225:793-806. [PMID: 31518434 DOI: 10.1111/nph.16195] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
In plants, rubisco activase (Rca) regulates rubisco by removing inhibitory molecules such as ribulose-1,5-bisphosphate (RuBP). In cyanobacteria, a homologous protein (activase-like cyanobacterial protein, ALC), contains a distinctive C-terminal fusion resembling the small-subunit of rubisco. Although cyanobacterial rubisco is believed to be less sensitive to RuBP inhibition, the ALC is widely distributed among diverse cyanobacteria. Using microscopy, biochemistry and molecular biology, the cellular localization of the ALC, its effect on carboxysome/cell ultrastructure in Fremyella diplosiphon, and its function in vitro were studied. Bioinformatic analysis uncovered evolutionary relationships between the ALC and rubisco. ALC localizes to carboxysomes and exhibits ATPase activity. Furthermore, the ALC induces rubisco aggregation in a manner similar to that of another carboxysomal protein, M35, and this activity is affected by ATP. An alc deletion mutant showed modified cell morphology when grown under enriched CO2 and impaired regulation of carboxysome biogenesis, without affecting growth rate. Carbamylation of Fremyella recombinant rubisco was inhibited by RuBP, but this inhibition was not relieved by the ALC. The ALC does not appear to function like a canonical Rca; instead, it exerts an effect on the response to CO2 availability at the level of a metabolic module, the carboxysome, through rubisco network formation, and carboxysome organization.
Collapse
Affiliation(s)
- Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brandon A Rohnke
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ana C O Belza
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Matthew R Melnicki
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| |
Collapse
|
19
|
Sun N, Han X, Xu M, Kaplan A, Espie GS, Mi H. A thylakoid-located carbonic anhydrase regulates CO 2 uptake in the cyanobacterium Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2019; 222:206-217. [PMID: 30383301 DOI: 10.1111/nph.15575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrases (CAs) are involved in CO2 uptake and conversion, a fundamental process in photosynthetic organisms. Nevertheless, the mechanism underlying the regulation of CO2 uptake and intracellular conversion in cyanobacteria is largely unknown. We report the characterization of a previously unrecognized thylakoid-located CA Slr0051 (EcaB) from the cyanobacterium Synechocystis sp. PCC 6803, which possesses CA activity to regulate CO2 uptake. Inactivation of ecaB stimulated CO2 hydration in the thylakoids, suppressed by the classical CA inhibitor acetazolamide. Absence of ecaB increased the reduced state of the photosynthetic electron transport system, lowered the rate of photosynthetic O2 evolution at high light (HL) and pH, and decreased the cellular affinity for extracellular inorganic carbon. Furthermore, EcaB was upregulated in cells grown at limiting CO2 concentration or HL in tandem with CupA. EcaB is mainly located in the thylakoid membranes where it interacts with CupA and CupB involved in CO2 uptake by converting it to bicarbonate. We propose that modulation of the EcaB level and activity in response to CO2 changes, illumination or pH reversibly regulates its conversion to HCO3 by the two CO2 -uptake systems (CupA, CupB), dissipating the excess HCO3- and alleviating photoinhibition, and thereby optimizes photosynthesis, especially under HL and alkaline conditions.
Collapse
Affiliation(s)
- Nan Sun
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xunling Han
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
| | - Min Xu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
| | - Aaron Kaplan
- Department Plant and Environmental Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - George S Espie
- Department of Biology, University of Toronto, Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 300 Fenglin Road, Shanghai, 200032, China
| |
Collapse
|
20
|
Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS. The small RbcS-like domains of the β-carboxysome structural protein CcmM bind RubisCO at a site distinct from that binding the RbcS subunit. J Biol Chem 2018; 294:2593-2603. [PMID: 30591587 DOI: 10.1074/jbc.ra118.006330] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Carboxysomes are compartments in bacterial cells that promote efficient carbon fixation by sequestering RubisCO and carbonic anhydrase within a protein shell that impedes CO2 escape. The key to assembling this protein complex is CcmM, a multidomain protein whose C-terminal region is required for RubisCO recruitment. This CcmM region is built as a series of copies (generally 3-5) of a small domain, CcmMS, joined by unstructured linkers. CcmMS domains have weak, but significant, sequence identity to RubisCO's small subunit, RbcS, suggesting that CcmM binds RubisCO by displacing RbcS. We report here the 1.35-Å structure of the first Thermosynechococcus elongatus CcmMS domain, revealing that it adopts a compact, well-defined structure that resembles that of RbcS. CcmMS, however, lacked key RbcS RubisCO-binding determinants, most notably an extended N-terminal loop. Nevertheless, individual CcmMS domains are able to bind RubisCO in vitro with 1.16 μm affinity. Two or four linked CcmMS domains did not exhibit dramatic increases in this affinity, implying that short, disordered linkers may frustrate successive CcmMS domains attempting to simultaneously bind a single RubisCO oligomer. Size-exclusion chromatography-coupled right-angled light scattering (SEC-RALS) and native MS experiments indicated that multiple CcmMS domains can bind a single RubisCO holoenzyme and, moreover, that RbcS is not released from these complexes. CcmMS bound equally tightly to a RubisCO variant in which the α/β domain of RbcS was deleted, suggesting that CcmMS binds RubisCO independently of its RbcS subunit. We propose that, instead, the electropositive CcmMS may bind to an extended electronegative pocket between RbcL dimers.
Collapse
Affiliation(s)
- Patrick Ryan
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Taylor J B Forrester
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Charles Wroblewski
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Tristan M G Kenney
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| |
Collapse
|
21
|
MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. eLife 2018; 7:39723. [PMID: 30520729 PMCID: PMC6328274 DOI: 10.7554/elife.39723] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022] Open
Abstract
Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria. Cyanobacteria are tiny organisms that can harness the energy of the sun to power their cells. Many of the tools required for this complex photosynthetic process are packaged into small compartments inside the cell, the carboxysomes. In Synechococcus elongatus, a cyanobacterium that is shaped like a rod, the carboxysomes are positioned at regular intervals along the length of the cell. This ensures that, when the bacterium splits itself in half to reproduce, both daughter cells have the same number of carboxysomes. Researchers know that, in S. elongatus, a protein called McdA can oscillate from one end of the cell to the other. This protein is responsible for the carboxysomes being in the right place, and some scientists believe that it helps to create an internal skeleton that anchors and drags the compartments into position. Here, MacCready et al. propose another mechanism and, by combining various approaches, identify a new partner for McdA. This protein, called McdB, is present on the carboxysomes. McdB also binds to McdA, which itself attaches to the nucleoid – the region in the cell that contains the DNA. McdB forces McdA to release itself from DNA, causing the protein to reposition itself along the nucleoid. Because McdB attaches to McdA, the carboxysomes then follow suit, constantly seeking the highest concentrations of McdA bound to nearby DNA. Instead of relying on a cellular skeleton, these two proteins can organize themselves on their own using the nucleoid as a scaffold; in turn, they distribute carboxysomes evenly along the length of a cell. Plants also obtain their energy from the sun via photosynthesis, but they do not carry carboxysomes. Scientists have tried to introduce these compartments inside plant cells, hoping that it could generate crops with higher yields. Knowing how carboxysomes are organized so they can be passed down from one generation to the next could be important for these experiments.
Collapse
Affiliation(s)
- Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Eric J Young
- Department of Biochemistry, Michigan State University, East Lansing, United States
| | - Longhua Hu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | | | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Daniel C Ducat
- Department of Biochemistry, Michigan State University, East Lansing, United States.,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| |
Collapse
|
22
|
Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
Collapse
Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
23
|
Slininger Lee M, Tullman-Ercek D. Practical considerations for the encapsulation of multi-enzyme cargos within the bacterial microcompartment for metabolic engineering. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
24
|
Niederhuber MJ, Lambert TJ, Yapp C, Silver PA, Polka JK. Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix. Mol Biol Cell 2017; 28:2734-2745. [PMID: 28963440 PMCID: PMC5620380 DOI: 10.1091/mbc.e17-01-0069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 11/11/2022] Open
Abstract
Carbon fixation in cyanobacteria makes a major contribution to the global carbon cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 from the atmosphere. The protein responsible for the organization of this lattice in beta-type carboxysomes of the freshwater cyanobacterium Synechococcus elongatus, CcmM, occurs in two isoforms thought to localize differentially within the carboxysome matrix. Here we use wide-field time-lapse and three-dimensional structured illumination microscopy (3D-SIM) to study the recruitment and localization of these two isoforms. We demonstrate that this superresolution technique is capable of distinguishing the localizations of the outer protein shell of the carboxysome and its internal cargo. We develop an automated analysis pipeline to analyze and quantify 3D-SIM images and generate a population-level description of the carboxysome shell protein, RuBisCO, and CcmM isoform localization. We find that both CcmM isoforms have similar spatial and temporal localization, prompting a revised model of the internal arrangement of the β-carboxysome.
Collapse
Affiliation(s)
- Matthew J Niederhuber
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Clarence Yapp
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Jessica K Polka
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| |
Collapse
|
25
|
Turmo A, Gonzalez-Esquer CR, Kerfeld CA. Carboxysomes: metabolic modules for CO2 fixation. FEMS Microbiol Lett 2017; 364:4082729. [DOI: 10.1093/femsle/fnx176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/12/2017] [Indexed: 11/13/2022] Open
|
26
|
Kaplan A. On the cradle of CCM research: discovery, development, and challenges ahead. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3785-3796. [PMID: 28520892 DOI: 10.1093/jxb/erx122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Herein, 40 years after its discovery, I briefly and critically survey the development of ideas that propelled research on CO2-concentrating mechanisms (CCMs; a term proposed by Dean Price) of phytoplankton, mainly focusing on cyanobacteria. This is not a comprehensive review on CCM research, but a personal view on the past developments and challenges that lie ahead.
Collapse
Affiliation(s)
- Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Israel
| |
Collapse
|
27
|
Rae BD, Long BM, Förster B, Nguyen ND, Velanis CN, Atkinson N, Hee WY, Mukherjee B, Price GD, McCormick AJ. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3717-3737. [PMID: 28444330 DOI: 10.1093/jxb/erx133] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals.
Collapse
Affiliation(s)
- Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Benedict M Long
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Christos N Velanis
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nicky Atkinson
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Wei Yih Hee
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Bratati Mukherjee
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Alistair J McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| |
Collapse
|
28
|
Klanchui A, Cheevadhanarak S, Prommeenate P, Meechai A. Exploring Components of the CO 2-Concentrating Mechanism in Alkaliphilic Cyanobacteria Through Genome-Based Analysis. Comput Struct Biotechnol J 2017; 15:340-350. [PMID: 28652895 PMCID: PMC5472144 DOI: 10.1016/j.csbj.2017.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/21/2017] [Accepted: 05/11/2017] [Indexed: 11/23/2022] Open
Abstract
In cyanobacteria, the CO2-concentrating mechanism (CCM) is a vital biological process that provides effective photosynthetic CO2 fixation by elevating the CO2 level near the active site of Rubisco. This process enables the adaptation of cyanobacteria to various habitats, particularly in CO2-limited environments. Although CCM of freshwater and marine cyanobacteria are well studied, there is limited information on the CCM of cyanobacteria living under alkaline environments. Here, we aimed to explore the molecular components of CCM in 12 alkaliphilic cyanobacteria through genome-based analysis. These cyanobacteria included 6 moderate alkaliphiles; Pleurocapsa sp. PCC 7327, Synechococcus spp., Cyanobacterium spp., Spirulina subsalsa PCC 9445, and 6 strong alkaliphiles (i.e. Arthrospira spp.). The results showed that both groups belong to β-cyanobacteria based on β-carboxysome shell proteins with form 1B of Rubisco. They also contained standard genes, ccmKLMNO cluster, which is essential for β-carboxysome formation. Most strains did not have the high-affinity Na+/HCO3- symporter SbtA and the medium-affinity ATP-dependent HCO3- transporter BCT1. Specifically, all strong alkaliphiles appeared to lack BCT1. Beside the transport systems, carboxysomal β-CA, CcaA, was absent in all alkaliphiles, except for three moderate alkaliphiles: Pleurocapsa sp. PCC 7327, Cyanobacteriumstranieri PCC 7202, and Spirulina subsalsa PCC 9445. Furthermore, comparative analysis of the CCM components among freshwater, marine, and alkaliphilic β-cyanobacteria revealed that the basic molecular components of the CCM in the alkaliphilic cyanobacteria seemed to share more degrees of similarity with freshwater than marine cyanobacteria. These findings provide a relationship between the CCM components of cyanobacteria and their habitats.
Collapse
Affiliation(s)
- Amornpan Klanchui
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Supapon Cheevadhanarak
- Division of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Pilot Plant Research and Development (BEC) Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| |
Collapse
|
29
|
The structure, kinetics and interactions of the β-carboxysomal β-carbonic anhydrase, CcaA. Biochem J 2016; 473:4559-4572. [DOI: 10.1042/bcj20160773] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/05/2016] [Accepted: 10/11/2016] [Indexed: 01/17/2023]
Abstract
CcaA is a β-carbonic anhydrase (CA) that is a component of the carboxysomes of a subset of β-cyanobacteria. This protein, which has a characteristic C-terminal extension of unknown function, is recruited to the carboxysome via interactions with CcmM, which is itself a γ-CA homolog with enzymatic activity in many, but not all cyanobacteria. We have determined the structure of CcaA from Synechocystis sp. PCC 6803 at 1.45 Å. In contrast with the dimer-of-dimers organization of most bacterial β-CAs, or the loose dimer-of-dimers-of-dimers organization found in the plant enzymes, CcaA shows a well-packed trimer-of-dimers organization. The proximal part of the characteristic C-terminal extension is ordered by binding at a site that passes through the two-fold symmetry axis shared with an adjacent dimer; as a result, only one of a pair of converging termini can be ordered at any given time. Docking in Rosetta failed to find well-packed solutions, indicating that formation of the CcaA/CcmM complex probably requires significant backbone movements in at least one of the binding partners. Surface plasmon resonance experiments showed that CcaA forms a complex with CcmM with sub-picomolar affinity, with contributions from residues in CcmM's αA helix and CcaA's C-terminal tail. Catalytic characterization showed CcaA to be among the least active β-CAs characterized to date, with activity comparable with the γ-CA, CcmM, it either complements or replaces. Intriguingly, the C-terminal tail appears to partly inhibit activity, possibly indicating a role in minimizing the activity of unencapsulated enzyme.
Collapse
|
30
|
Kupriyanova EV, Cho SM, Park YI, Pronina NA, Los DA. The complete genome of a cyanobacterium from a soda lake reveals the presence of the components of CO 2-concentrating mechanism. PHOTOSYNTHESIS RESEARCH 2016; 130:151-165. [PMID: 26908147 DOI: 10.1007/s11120-016-0235-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
At present geological epoch, the carbon concentrating mechanism (CCM) of cyanobacteria represents the obligatory tool for adaptation to low content of CO2 in the atmosphere and for the maintenance of sufficient photosynthetic activity. Functional CCM was found in modern cyanobacteria from different ecological niches. However, the presence of such mechanism in species that inhabit soda lakes is not obvious due to high content of inorganic carbon (C i) in the environment. Here we analyze CCM components that have been identified by sequencing of the whole genome of the alkaliphilic cyanobacterium Microcoleus sp. IPPAS B-353. The composition of the CCM components of Microcoleus is similar to that of 'model' β-cyanobacteria, freshwater and marine Synechococcus or Synechocystis spp. However, CahB1 protein of Microcoleus, which is the homolog of CcaA, the carboxysomal β-type carbonic anhydrase (CA) of β-cyanobacteria, appeared to be the only active CA located in cell envelopes. The conservative regions of CcmM, CahG (a homolog of archeal γ-CAs, Cam/CamH), and ChpX of Microcoleus possess single amino acid substitutions that may cause a lack of CA activities. Unlike model cyanobacteria, Microcoleus induces only one BicA-type bicarbonate transporter in response to C i limitation. The differences in the appearance of CCM components and in their characteristics between alkaliphilic Microcoleus and freshwater or marine cyanobacteria are described. The possible reasons for the maintenance of CCM components in cyanobacteria, which permanently live at high concentrations of C i in soda lakes, are discussed.
Collapse
Affiliation(s)
- Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276.
| | - Sung Mi Cho
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Natalia A Pronina
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
| |
Collapse
|
31
|
Chowdhury C, Chun S, Sawaya MR, Yeates TO, Bobik TA. The function of the PduJ microcompartment shell protein is determined by the genomic position of its encoding gene. Mol Microbiol 2016; 101:770-83. [PMID: 27561553 PMCID: PMC5003431 DOI: 10.1111/mmi.13423] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2016] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2-propanediol (1,2-PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2-PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2-PD transport. The crystal structure revealed that PduJ was nearly identical to that of PduA and, hence, offered no explanation for their differential functions. Interestingly, however, when a pduJ gene was placed at the pduA chromosomal locus, the PduJ protein acquired a new function, the ability to mediate 1,2-PD transport into the Pdu MCP. To our knowledge, these are the first studies to show that that gene location can determine the function of a MCP shell protein. We propose that gene location dictates protein-protein interactions essential to the function of the MCP shell.
Collapse
Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Sunny Chun
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Michael R. Sawaya
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
| | - Todd O. Yeates
- Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| |
Collapse
|
32
|
Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:66-75. [PMID: 27060669 DOI: 10.1016/j.pbi.2016.03.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 05/19/2023]
Abstract
All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.
Collapse
Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Matthew R Melnicki
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
33
|
Long BM, Rae BD, Rolland V, Förster B, Price GD. Cyanobacterial CO2-concentrating mechanism components: function and prospects for plant metabolic engineering. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:1-8. [PMID: 26999306 DOI: 10.1016/j.pbi.2016.03.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/25/2016] [Accepted: 03/02/2016] [Indexed: 05/21/2023]
Abstract
Global population growth is projected to outpace plant-breeding improvements in major crop yields within decades. To ensure future food security, multiple creative efforts seek to overcome limitations to crop yield. Perhaps the greatest limitation to increased crop yield is photosynthetic inefficiency, particularly in C3 crop plants. Recently, great strides have been made toward crop improvement by researchers seeking to introduce the cyanobacterial CO2-concentrating mechanism (CCM) into plant chloroplasts. This strategy recognises the C3 chloroplast as lacking a CCM, and being a primordial cyanobacterium at its essence. Hence the collection of solute transporters, enzymes, and physical structures that make cyanobacterial CO2-fixation so efficient are viewed as a natural source of genetic material for C3 chloroplast improvement. Also we highlight recent outstanding research aimed toward the goal of introducing a cyanobacterial CCM into C3 chloroplasts and consider future research directions.
Collapse
Affiliation(s)
- Benedict M Long
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
| | - Benjamin D Rae
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Vivien Rolland
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - G Dean Price
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
34
|
Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome. J Mol Biol 2016; 428:153-164. [DOI: 10.1016/j.jmb.2015.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/04/2015] [Accepted: 11/12/2015] [Indexed: 01/24/2023]
|
35
|
Bobik TA, Lehman BP, Yeates TO. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways. Mol Microbiol 2015; 98:193-207. [PMID: 26148529 PMCID: PMC4718714 DOI: 10.1111/mmi.13117] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Abstract
Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.
Collapse
Affiliation(s)
- Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Brent P. Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| |
Collapse
|
36
|
Bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments. Appl Environ Microbiol 2015; 81:8315-29. [PMID: 26407889 DOI: 10.1128/aem.02587-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics.
Collapse
|
37
|
Aussignargues C, Paasch BC, Gonzalez-Esquer R, Erbilgin O, Kerfeld CA. Bacterial microcompartment assembly: The key role of encapsulation peptides. Commun Integr Biol 2015; 8:e1039755. [PMID: 26478774 PMCID: PMC4594438 DOI: 10.1080/19420889.2015.1039755] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/14/2022] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (∼17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. Here, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.
Collapse
Affiliation(s)
| | - Bradley C Paasch
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA
| | | | - Onur Erbilgin
- Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA
| | - Cheryl A Kerfeld
- DOE Plant Research Laboratory; Michigan State University ; East Lansing, MI USA ; Department of Plant and Microbial Biology; University of California, Berkeley ; Berkeley, CA USA ; Physical Biosciences Division; Lawrence Berkeley National Laboratory ; Berkeley, CA USA ; Berkeley Synthetic Biology Institute ; Berkeley, CA USA
| |
Collapse
|
38
|
Kupriyanova EV, Samylina OS. CO2-concentrating mechanism and its traits in haloalkaliphilic cyanobacteria. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715010075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
39
|
Whitaker WR, Lee H, Arkin AP, Dueber JE. Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences. ACS Synth Biol 2015; 4:249-57. [PMID: 24931615 DOI: 10.1021/sb500003x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Genetic sequences ported into non-native hosts for synthetic biology applications can gain unexpected properties. In this study, we explored sequences functioning as ribosome binding sites (RBSs) within protein coding DNA sequences (CDSs) that cause internal translation, resulting in truncated proteins. Genome-wide prediction of bacterial RBSs, based on biophysical calculations employed by the RBS calculator, suggests a selection against internal RBSs within CDSs in Escherichia coli, but not those in Saccharomyces cerevisiae. Based on these calculations, silent mutations aimed at removing internal RBSs can effectively reduce truncation products from internal translation. However, a solution for complete elimination of internal translation initiation is not always feasible due to constraints of available coding sequences. Fluorescence assays and Western blot analysis showed that in genes with internal RBSs, increasing the strength of the intended upstream RBS had little influence on the internal translation strength. Another strategy to minimize truncated products from an internal RBS is to increase the relative strength of the upstream RBS with a concomitant reduction in promoter strength to achieve the same protein expression level. Unfortunately, lower transcription levels result in increased noise at the single cell level due to stochasticity in gene expression. At the low expression regimes desired for many synthetic biology applications, this problem becomes particularly pronounced. We found that balancing promoter strengths and upstream RBS strengths to intermediate levels can achieve the target protein concentration while avoiding both excessive noise and truncated protein.
Collapse
Affiliation(s)
- Weston R. Whitaker
- Departments
of Bioengineering, University of California, Berkeley, California 94720, United States
- The University of California, Berkeley and University of California, San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, United States
| | - Hanson Lee
- Departments
of Bioengineering, University of California, Berkeley, California 94720, United States
- Energy
Biosciences Institute, University of California, Berkeley, 2151 Berkeley
Way, Berkeley California 94704, United States
| | - Adam P. Arkin
- Departments
of Bioengineering, University of California, Berkeley, California 94720, United States
- Energy
Biosciences Institute, University of California, Berkeley, 2151 Berkeley
Way, Berkeley California 94704, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - John E. Dueber
- Departments
of Bioengineering, University of California, Berkeley, California 94720, United States
- Energy
Biosciences Institute, University of California, Berkeley, 2151 Berkeley
Way, Berkeley California 94704, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| |
Collapse
|
40
|
Burnap RL, Hagemann M, Kaplan A. Regulation of CO2 Concentrating Mechanism in Cyanobacteria. Life (Basel) 2015; 5:348-71. [PMID: 25636131 PMCID: PMC4390856 DOI: 10.3390/life5010348] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/31/2022] Open
Abstract
In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO2 and discuss mechanisms of inorganic carbon (Ci) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The structural components for several of the transport and uptake mechanisms are described and the progress towards elucidating their regulation is discussed in the context of studies, which have documented metabolomic changes in response to changes in Ci availability. Genes for several of the transport and uptake mechanisms are regulated by transcriptional regulators that are in the LysR-transcriptional regulator family and are known to act in concert with small molecule effectors, which appear to be well-known metabolites. Signals that trigger changes in gene expression and enzyme activity correspond to specific "regulatory metabolites" whose concentrations depend on the ambient Ci availability. Finally, emerging evidence for an additional layer of regulatory complexity involving small non-coding RNAs is discussed.
Collapse
Affiliation(s)
- Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Martin Hagemann
- Institute Biosciences, Department Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, Rostock D-18059, Germany.
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| |
Collapse
|
41
|
Bacterial microcompartments and the modular construction of microbial metabolism. Trends Microbiol 2015; 23:22-34. [DOI: 10.1016/j.tim.2014.10.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/22/2023]
|
42
|
Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 2014; 10:e1003898. [PMID: 25340524 PMCID: PMC4207490 DOI: 10.1371/journal.pcbi.1003898] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/09/2014] [Indexed: 01/21/2023] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications. Some enzymatic transformations have undesirable side reactions, produce toxic or volatile intermediates, or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space, as in the membrane-bound organelles of eukaryotes. Recently, it was discovered that bacteria also form organelles–bacterial microcompartments (BMCs)–composed of a protein shell that surrounds functionally related enzymes. BMCs long evaded detection because they typically form only in the presence of the substrate they metabolize, and they can only be visualized by electron microscopy. A few BMCs have been experimentally characterized; they have diverse functions in CO2 fixation, pathogenesis, and niche colonization. While the encapsulated enzymes differ among functionally distinct BMCs, the shell architecture is conserved. This enables their detection computationally, as genes for shell proteins are typically nearby genes for the encapsulated enzymes. We developed a novel algorithm to comprehensively identify and categorize BMCs in sequenced bacterial genomes. We show that BMCs are often encoded adjacent to genes that play supporting roles to the organelle's function. Our results provide the first glimpse of the extent of BMC metabolic diversity and will inform design of genetic modules encoding BMCs for introduction of new metabolic functions in a plug-and-play approach.
Collapse
Affiliation(s)
- Seth D. Axen
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Onur Erbilgin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Berkeley Synthetic Biology Institute, Berkeley, California, United States of America
- * E-mail: ,
| |
Collapse
|
43
|
de Araujo C, Arefeen D, Tadesse Y, Long BM, Price GD, Rowlett RS, Kimber MS, Espie GS. Identification and characterization of a carboxysomal γ-carbonic anhydrase from the cyanobacterium Nostoc sp. PCC 7120. PHOTOSYNTHESIS RESEARCH 2014; 121:135-50. [PMID: 24907906 DOI: 10.1007/s11120-014-0018-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 05/26/2023]
Abstract
Carboxysomes are proteinaceous microcompartments that encapsulate carbonic anhydrase (CA) and ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco); carboxysomes, therefore, catalyze reversible HCO3 (-) dehydration and the subsequent fixation of CO2. The N- and C-terminal domains of the β-carboxysome scaffold protein CcmM participate in a network of protein-protein interactions that are essential for carboxysome biogenesis, organization, and function. The N-terminal domain of CcmM in the thermophile Thermosynechococcus elongatus BP-1 is also a catalytically active, redox regulated γ-CA. To experimentally determine if CcmM from a mesophilic cyanobacterium is active, we cloned, expressed and purified recombinant, full-length CcmM from Nostoc sp. PCC 7120 as well as the N-terminal 209 amino acid γ-CA-like domain. Both recombinant proteins displayed ethoxyzolamide-sensitive CA activity in mass spectrometric assays, as did the carboxysome-enriched TP fraction. NstCcmM209 was characterized as a moderately active and efficient γ-CA with a k cat of 2.0 × 10(4) s(-1) and k cat/K m of 4.1 × 10(6) M(-1) s(-1) at 25 °C and pH 8, a pH optimum between 8 and 9.5 and a temperature optimum spanning 25-35 °C. NstCcmM209 also catalyzed the hydrolysis of the CO2 analog carbonyl sulfide. Circular dichroism and intrinsic tryptophan fluorescence analysis demonstrated that NstCcmM209 was progressively and irreversibly denatured above 50 °C. NstCcmM209 activity was inhibited by the reducing agent tris(hydroxymethyl)phosphine, an effect that was fully reversed by a molar excess of diamide, a thiol oxidizing agent, consistent with oxidative activation being a universal regulatory mechanism of CcmM orthologs. Immunogold electron microscopy and Western blot analysis of TP pellets indicated that Rubisco and CcmM co-localize and are concentrated in Nostoc sp. PCC 7120 carboxysomes.
Collapse
Affiliation(s)
- Charlotte de Araujo
- Department of Cell & Systems Biology, University of Toronto, Mississauga, ON, Canada
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Nishimura T, Yamaguchi O, Takatani N, Maeda SI, Omata T. In vitro and in vivo analyses of the role of the carboxysomal β-type carbonic anhydrase of the cyanobacterium Synechococcus elongatus in carboxylation of ribulose-1,5-bisphosphate. PHOTOSYNTHESIS RESEARCH 2014; 121:151-7. [PMID: 24585024 DOI: 10.1007/s11120-014-9986-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/16/2014] [Indexed: 05/09/2023]
Abstract
The carboxylase activities of crude carboxysome preparations obtained from the wild-type Synechococcus elongatus strain PCC 7942 strain and the mutant defective in the carboxysomal carbonic anhydrase (CA) were compared. The carboxylation reaction required high concentrations of bicarbonate and was not even saturated at 50 mM bicarbonate. With the initial concentrations of 50 mM and 25 mM for bicarbonate and ribulose-1,5-bisphosphate (RuBP), respectively, the initial rate of RuBP carboxylation by the mutant carboxysome (0.22 μmol mg(-1) protein min(-1)) was only 30 % of that observed for the wild-type carboxysomes (0.71 μmol mg(-1) protein min(-1)), indicating the importance of the presence of CA in efficient catalysis by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). While the mutant defective in the ccmLMNO genes, which lacks the carboxysome structure, could grow under aeration with 2 % (v/v) CO2 in air, the mutant defective in ccaA as well as ccmLMNO required 5 % (v/v) CO2 for growth, indicating that the cytoplasmically localized CcaA helped utilization of CO2 by the cytoplasmically localized Rubisco by counteracting the action of the CO2 hydration mechanism. The results predict that overexpression of Rubisco would hardly enhance CO2 fixation by the cyanobacterium at CO2 levels lower than 5 %, unless Rubisco is properly organized into carboxysomes.
Collapse
Affiliation(s)
- Takashi Nishimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | | | | | | | | |
Collapse
|
45
|
Lin MT, Occhialini A, Andralojc JP, Devonshire J, Hines KM, Parry MAJ, Hanson MR. β-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:1-12. [PMID: 24810513 PMCID: PMC4080790 DOI: 10.1111/tpj.12536] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/15/2014] [Indexed: 05/18/2023]
Abstract
The photosynthetic efficiency of C3 plants suffers from the reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) with O2 instead of CO2 , leading to the costly process of photorespiration. Increasing the concentration of CO2 around Rubisco is a strategy used by photosynthetic prokaryotes such as cyanobacteria for more efficient incorporation of inorganic carbon. Engineering the cyanobacterial CO2 -concentrating mechanism, the carboxysome, into chloroplasts is an approach to enhance photosynthesis or to compartmentalize other biochemical reactions to confer new capabilities on transgenic plants. We have chosen to explore the possibility of producing β-carboxysomes from Synechococcus elongatus PCC7942, a model freshwater cyanobacterium. Using the agroinfiltration technique, we have transiently expressed multiple β-carboxysomal proteins (CcmK2, CcmM, CcmL, CcmO and CcmN) in Nicotiana benthamiana with fusions that target these proteins into chloroplasts, and that provide fluorescent labels for visualizing the resultant structures. By confocal and electron microscopic analysis, we have observed that the shell proteins of the β-carboxysome are able to assemble in plant chloroplasts into highly organized assemblies resembling empty microcompartments. We demonstrate that a foreign protein can be targeted with a 17-amino-acid CcmN peptide to the shell proteins inside chloroplasts. Our experiments establish the feasibility of introducing carboxysomes into chloroplasts for the potential compartmentalization of Rubisco or other proteins.
Collapse
Affiliation(s)
- Myat T. Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | | | - John P. Andralojc
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Jean Devonshire
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Kevin M. Hines
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Martin A. J. Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
46
|
Whitehead L, Long BM, Price GD, Badger MR. Comparing the in vivo function of α-carboxysomes and β-carboxysomes in two model cyanobacteria. PLANT PHYSIOLOGY 2014; 165:398-411. [PMID: 24642960 PMCID: PMC4012598 DOI: 10.1104/pp.114.237941] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/10/2014] [Indexed: 05/19/2023]
Abstract
The carbon dioxide (CO2)-concentrating mechanism of cyanobacteria is characterized by the occurrence of Rubisco-containing microcompartments called carboxysomes within cells. The encapsulation of Rubisco allows for high-CO2 concentrations at the site of fixation, providing an advantage in low-CO2 environments. Cyanobacteria with Form-IA Rubisco contain α-carboxysomes, and cyanobacteria with Form-IB Rubisco contain β-carboxysomes. The two carboxysome types have arisen through convergent evolution, and α-cyanobacteria and β-cyanobacteria occupy different ecological niches. Here, we present, to our knowledge, the first direct comparison of the carboxysome function from α-cyanobacteria (Cyanobium spp. PCC7001) and β-cyanobacteria (Synechococcus spp. PCC7942) with similar inorganic carbon (Ci; as CO2 and HCO3-) transporter systems. Despite evolutionary and structural differences between α-carboxysomes and β-carboxysomes, we found that the two strains are remarkably similar in many physiological parameters, particularly the response of photosynthesis to light and external Ci and their modulation of internal ribulose-1,5-bisphosphate, phosphoglycerate, and Ci pools when grown under comparable conditions. In addition, the different Rubisco forms present in each carboxysome had almost identical kinetic parameters. The conclusions indicate that the possession of different carboxysome types does not significantly influence the physiological function of these species and that similar carboxysome function may be possessed by each carboxysome type. Interestingly, both carboxysome types showed a response to cytosolic Ci, which is of higher affinity than predicted by current models, being saturated by 5 to 15 mm Ci. This finding has bearing on the viability of transplanting functional carboxysomes into the C3 chloroplast.
Collapse
Affiliation(s)
- Lynne Whitehead
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - Benedict M. Long
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - G. Dean Price
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - Murray R. Badger
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| |
Collapse
|
47
|
Mangan NM, Brenner MP. Systems analysis of the CO2 concentrating mechanism in cyanobacteria. eLife 2014; 3:e02043. [PMID: 24842993 PMCID: PMC4027813 DOI: 10.7554/elife.02043] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/12/2014] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteria are photosynthetic bacteria with a unique CO2 concentrating mechanism (CCM), enhancing carbon fixation. Understanding the CCM requires a systems level perspective of how molecular components work together to enhance CO2 fixation. We present a mathematical model of the cyanobacterial CCM, giving the parameter regime (expression levels, catalytic rates, permeability of carboxysome shell) for efficient carbon fixation. Efficiency requires saturating the RuBisCO reaction, staying below saturation for carbonic anhydrase, and avoiding wasteful oxygenation reactions. We find selectivity at the carboxysome shell is not necessary; there is an optimal non-specific carboxysome shell permeability. We compare the efficacy of facilitated CO2 uptake, CO2 scavenging, and HCO3- transport with varying external pH. At the optimal carboxysome permeability, contributions from CO2 scavenging at the cell membrane are small. We examine the cumulative benefits of CCM spatial organization strategies: enzyme co-localization and compartmentalization.
Collapse
Affiliation(s)
- Niall M Mangan
- School of Engineering and Applied Sciences and Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, United States
| | - Michael P Brenner
- School of Engineering and Applied Sciences and Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, United States
| |
Collapse
|
48
|
Carboxysomes – Sequestering RubisCO for Efficient Carbon Fixation. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
49
|
Abstract
Cyanobacteria and some chemoautotrophic bacteria enhance their carbon fixation efficiency by actively concentrating bicarbonate within their cytosol. However, converting bicarbonate into carbon dioxide - the form required by RubisCO - would result in its rapid escape through cellular membranes. These organisms resolve this dilemma by sequestering RubisCO behind a semi-permeable protein shell; the resulting large insoluble bodies are known as carboxysomes. For the carbon concentrating mechanism to function, there is an absolute requirement for carbonic anhydrase activity within the carboxysome to convert the bicarbonate to cabon dioxide, and a simultaneous requirement that minimal carbonic anhydrase activity be found within the cystol. Carboxysomal carbomic anhydrases therefore contain additional motifs and domains that generally mediate protein-protein interactions, or encapsulation dependent activation mechanisms. Carboxysomes are found in two deeply divergent varieties. Alpha-Carboxysomes contain a β-carbonic anhydrase, CsoSCA, which is so divergent from canonical β-carbonic anhydrases that it was originally thought to be the founding member of a new class. Beta carboxysomes have CcmM whose N-terminal domain is an active γ-carbonic ahydrase in some strains, but in others has lost all activity and functions primarily as a protein complex assembly scaffold; in addition, a subset of β-carboxysomes also contain the β-carbonic anhydrase CcaA - either in addition to, or instead of, an active CcmM. Here we explore the structures, activities and interactions mediated by the three known carboxysomal carbonic anhydrases, and discuss the mechanisms by which they are recruited to the carboxysome.
Collapse
|
50
|
Kupriyanova EV, Sinetova MA, Cho SM, Park YI, Los DA, Pronina NA. CO2-concentrating mechanism in cyanobacterial photosynthesis: organization, physiological role, and evolutionary origin. PHOTOSYNTHESIS RESEARCH 2013; 117:133-146. [PMID: 23733616 DOI: 10.1007/s11120-013-9860-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/25/2013] [Indexed: 06/02/2023]
Abstract
The cellular and molecular organization of the CO2-concentrating mechanism (CCM) of cyanobacteria is reviewed. The primary processes of uptake, translocation, and accumulation of inorganic carbon (Ci) near the active site of carbon assimilation by the enzyme ribulose-1,5-bisphosphate carboxylase in the C3 cycle in cyanobacteria are described as one of the specialized forms of CO2 concentration which occurs in some photoautotrophic cells. The existence of this form of CO2 concentration expands our understanding of photosynthetic Ci assimilation. The means of supplying Ci to the C3 cycle in cyanobacteria is not by simple diffusion into the cell, but it is the result of coordinated functions of high-affinity systems for the uptake of CO2 and bicarbonate, as well as intracellular CO2/HCO3 (-) interconversions by carbonic anhydrases. These biochemical events are under genetic control, and they serve to maintain cellular homeostasis and adaptation to CO2 limitation. Here we describe the organization of the CCM in cyanobacteria with a special focus on the CCM of relict halo- and alkaliphilic cyanobacteria of soda lakes. We also assess the role of the CCM at the levels of the organism, the biosphere, and evolution.
Collapse
Affiliation(s)
- Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street, 35, Moscow, 127276, Russia
| | | | | | | | | | | |
Collapse
|