Expression of foreign type I ribulose-1,5-bisphosphate carboxylase/ oxygenase (EC 4.1.1.39) stimulates photosynthesis in cyanobacterium Synechococcus PCC7942 cells

2006 ◽  
Vol 88 (3) ◽  
pp. 287-297 ◽  
Author(s):  
T. Iwaki ◽  
K. Haranoh ◽  
N. Inoue ◽  
K. Kojima ◽  
R. Satoh ◽  
...  
Keyword(s):  
Type I ◽  
Bisphosphate Carboxylase ◽  
Synechococcus Pcc7942

The transcription of the cbb operon in Nitrosomonas europaea

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1869-1879 ◽  
Author(s):  
Xueming Wei ◽  
Luis A. Sayavedra-Soto ◽  
Daniel J. Arp
Keyword(s):  
Carbon Source ◽  
Regulatory Protein ◽  
Carbon Assimilation ◽  
Nitrosomonas Europaea ◽  
Gene Organization ◽  
Carbon Limitation ◽  
Type I ◽  
Ribulose Bisphosphate Carboxylase ◽  
External Energy ◽  
Bisphosphate Carboxylase

Nitrosomonas europaea is an aerobic ammonia-oxidizing bacterium that participates in the C and N cycles. N. europaea utilizes CO2 as its predominant carbon source, and is an obligate chemolithotroph, deriving all the reductant required for energy and biosynthesis from the oxidation of ammonia (NH3) to nitrite (). This bacterium fixes carbon via the Calvin–Benson–Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). The RubisCO operon is composed of five genes, cbbLSQON. This gene organization is similar to that of the operon for ‘green-like’ type I RubisCOs in other organisms. The cbbR gene encoding the putative regulatory protein for RubisCO transcription was identified upstream of cbbL. This study showed that transcription of cbb genes was upregulated when the carbon source was limited, while amo, hao and other energy-harvesting-related genes were downregulated. N. europaea responds to carbon limitation by prioritizing resources towards key components for carbon assimilation. Unlike the situation for amo genes, NH3 was not required for the transcription of the cbb genes. All five cbb genes were only transcribed when an external energy source was provided. In actively growing cells, mRNAs from the five genes in the RubisCO operon were present at different levels, probably due to premature termination of transcription, rapid mRNA processing and mRNA degradation.

Thioalkalivibrio sulfidiphilus sp. nov., a haloalkaliphilic, sulfur-oxidizing gammaproteobacterium from alkaline habitats

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1884-1889 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Maria S. Muntyan ◽  
Anzhela N. Panteleeva ◽  
Gerard Muyzer
Keyword(s):  
Soda Lake ◽  
16S Rrna Gene Sequencing ◽  
Salinity Range ◽  
Rrna Gene ◽  
Type I ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Content Type ◽  
Link Type ◽  
Sulfur Oxidizing

A moderately salt-tolerant and obligately alkaliphilic, chemolithoautotrophic sulfur-oxidizing bacterium, strain HL-EbGr7T, was isolated from a full-scale bioreactor removing H2S from biogas under oxygen-limited conditions. Another strain, ALJ17, closely related to HL-EbGr7T, was isolated from a Kenyan soda lake. Cells of the isolates were relatively long, slender rods, motile by a polar flagellum. Although both strains were obligately aerobic, micro-oxic conditions were preferred, especially at the beginning of growth. Chemolithoautotrophic growth was observed with sulfide and thiosulfate in a pH range of 8.0–10.5 (optimum at pH 10.0) and a salinity range of 0.2–1.5 M total Na+ (optimum at 0.4 M). The genome sequence of strain HL-EbGr7T demonstrated the presence of genes encoding the reverse Dsr pathway and a truncated Sox pathway for sulfur oxidation and enzymes of the Calvin–Benson cycle of autotrophic CO2 assimilation with ribulose-bisphosphate carboxylase/oxygenase (RuBisCO) type I. The dominant cellular fatty acids were C18 : 1ω7, C16 : 0 and C19 : 0 cyclo. Based on 16S rRNA gene sequencing, the two strains belonged to a single phylotype within the genus Thioalkalivibrio in the Gammaproteobacteria . Despite being related most closely to Thioalkalivibrio denitrificans , the isolates were unable to grow by denitrification. On the basis of phenotypic and phylogenetic analysis, the novel isolates are proposed to represent a novel species, Thioalkalivibrio sulfidiphilus sp. nov., with the type strain HL-EbGr7T ( = NCCB 100376T  = UNIQEM U246T).

scholarly journals Phylogeny and Functional Expression of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from the Autotrophic Ammonia-Oxidizing Bacterium Nitrosospira sp.Isolate 40KI

2002 ◽  
Vol 184 (2) ◽  
pp. 468-478 ◽  
Author(s):  
Janne B. Utåker ◽  
Kjell Andersen ◽  
Ågot Aakra ◽  
Birgitte Moen ◽  
Ingolf F. Nes
Keyword(s):  
Ralstonia Eutropha ◽  
Sequence Similarity ◽  
Large Subunit ◽  
Expression System ◽  
Functional Expression ◽  
Rrna Gene ◽  
Type I ◽  
Ammonia Oxidizing Bacteria ◽  
High Sequence Similarity ◽  
Bisphosphate Carboxylase

ABSTRACT The autotrophic ammonia-oxidizing bacteria (AOB), which play an important role in the global nitrogen cycle, assimilate CO2 by using ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we describe the first detailed study of RubisCO (cbb) genes and proteins from the AOB. The cbbLS genes from Nitrosospira sp. isolate 40KI were cloned and sequenced. Partial sequences of the RubisCO large subunit (CbbL) from 13 other AOB belonging to the β and γ subgroups of the class Proteobacteria are also presented. All except one of the β-subgroup AOB possessed a red-like type I RubisCO with high sequence similarity to the Ralstonia eutropha enzyme. All of these new red-like RubisCOs had a unique six-amino-acid insert in CbbL. Two of the AOB, Nitrosococcus halophilus Nc4 and Nitrosomonas europaea Nm50, had a green-like RubisCO. With one exception, the phylogeny of the AOB CbbL was very similar to that of the 16S rRNA gene. The presence of a green-like RubisCO in N. europaea was surprising, as all of the other β-subgroup AOB had red-like RubisCOs. The green-like enzyme of N. europaea Nm50 was probably acquired by horizontal gene transfer. Functional expression of Nitrosospira sp. isolate 40KI RubisCO in the chemoautotrophic host R. eutropha was demonstrated. Use of an expression vector harboring the R. eutropha cbb control region allowed regulated expression of Nitrosospira sp. isolate 40KI RubisCO in an R. eutropha cbb deletion strain. The Nitrosospira RubisCO supported autotrophic growth of R. eutropha with a doubling time of 4.6 h. This expression system may allow further functional analysis of AOB cbb genes.

scholarly journals Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

2006 ◽  
Vol 72 (3) ◽  
pp. 2050-2063 ◽  
Author(s):  
Shawn R. Starkenburg ◽  
Patrick S. G. Chain ◽  
Luis A. Sayavedra-Soto ◽  
Loren Hauser ◽  
Miriam L. Land ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Rhodopseudomonas Palustris ◽  
Type I ◽  
Nitrite Oxidation ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Gene Copies ◽  
Nitrite Oxidizing Bacteria ◽  
Genes Encoding ◽  
Nitrite Oxidoreductase

ABSTRACT The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

scholarly journals Chloroplast Genome Evolution in the Genus Avena

Genetics ◽  
1987 ◽  
Vol 116 (4) ◽  
pp. 613-621
Author(s):  
Koji Murai ◽  
Koichiro Tsunewaki
Keyword(s):  
Chloroplast Genome ◽  
Restriction Site ◽  
Physical Map ◽  
Fragment Size ◽  
Large Subunit ◽  
Single Copy ◽  
Rbcl Gene ◽  
Type I ◽  
Bisphosphate Carboxylase ◽  
Chloroplast Genomes

ABSTRACT The genus Avena contains five different chloroplast genomes, I-V. A physical map of chloroplast (ct) DNA of Avena sativa (type I chloroplast genome) was constructed using three restriction endonucleases, PstI, SalI and SmaI. This genome is ca. 135.5 kbp in size, and contains two inverted repeats of ca. 22.5 kbp each, separated by a large (ca. 79.0 kbp) and small (ca. 12.5 kbp) single copy region. The rbcL gene which codes for the large subunit of ribulose 1,5-bisphosphate carboxylase, was located in the map. Restriction fragment patterns of all five chloroplast genomes were compared, and among them five fragment size and five restriction site mutations were disclosed. Four site mutations were found in two or more chloroplast genomes, the other site and five fragment size mutations were specific to one or another of the chloroplast genomes. A dendrogram showing phylogenetic relationships among the five chloroplast genomes, based on the distribution of the common and specific mutations among them, indicates that chloroplast genome divergence characterized by three restriction site mutations occurred first between two diploid groups, each carrying A and C genome (nuclear), respectively, followed by further speciation in each group.

The functioning of the CO2 concentrating mechanism in several cyanobacterial strains: a review of general physiological characteristics, genes, proteins, and recent advances

1998 ◽  
Vol 76 (6) ◽  
pp. 973-1002 ◽  
Author(s):  
G Dean Price ◽  
Dieter Sültemeyer ◽  
Barbara Klughammer ◽  
Martha Ludwig ◽  
Murray R Badger
Keyword(s):  
Distinct Type ◽  
Ribulose Bisphosphate Carboxylase ◽  
Genome Database ◽  
Bisphosphate Carboxylase ◽  
Blue Green Algae ◽  
Synechocystis Pcc6803 ◽  
Concentrating Mechanism ◽  
Recent Advances ◽  
Ribulose Bisphosphate Carboxylase Oxygenase ◽  
Synechococcus Pcc7942

Cyanobacteria (blue-green algae) possess an environmental adaptation for survival at low CO2 concentrations. The adaptation is known as a CO2 concentrating mechanism (CCM), and it functions to actively transport and accumulate inorganic carbon ( and CO2; Ci) within the cell and then uses this Ci pool to provide elevated CO2 concentrations around the primary CO2-fixing enzyme, ribulose bisphosphate carboxylase-oxygenase (Rubisco). It appears that the site of CO2 elevation is within a unique microcompartment known as the carboxysome, which is a proteinaceous polyhedral body that contains most, if not all, of the Rubisco within the cell. This review covers comparative aspects of physiology, genetics, and proteins involved in the cyanobacterial CCM with particular focus on recent advances. This review highlights information on three strains of unicellular cyanobacteria, namely Synechocystis PCC6803 (freshwater strain; for which a full genome database is now available), Synechococcus PCC7002 (coastal marine strain) and Synechococcus PCC7942 (freshwater strain). Genes that may be involved in the CCM, directly or indirectly, are summarized in tabular form. For Synechocystis PCC6803, the number of genes related to CCM activity is now in excess of 50; however, 19 of these components have the potential to code for several distinct type-1, NADH dehydrogenase complexes.Key words: cyanobacteria, CO2 concentrating mechanism, carboxysomes, genes, photosynthesis, transporters.

Proteomic assessment of an established technique for carboxysome enrichment from Synechococcus PCC7942

2005 ◽  
Vol 83 (7) ◽  
pp. 746-757 ◽  
Author(s):  
Ben M Long ◽  
G Dean Price ◽  
Murray R Badger
Keyword(s):  
Protein Identification ◽  
Bisphosphate Carboxylase ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Enrichment Technique ◽  
Concentrating Mechanism ◽  
Key Enzyme ◽  
Synechococcus Pcc7942 ◽  
Tof Ms

Carboxysomes are protein-bound, polyhedral microbodies within cyanobacteria, containing the key enzyme for photosynthetic CO2 fixation, ribulose-1,5-bisphosphate carboxylase–oxygenase (Rubisco). Sequencing of cyanobacterial genomes has revealed that cyanobacteria possess one or other of two types of carboxysomes. Cyanobacteria containing form 1A Rubisco possess α-carboxysomes, while those with form 1B Rubisco possess β-carboxysomes. Given the central importance of carboxysomes in the CO2-concentrating mechanism of cyanobacteria, understanding the nature and composition of these structures is of considerable importance. In an effort to develop techniques for the characterization of the structure of β-carboxysomes, particularly the outer protein shell, we have undertaken a proteomic assessment of the Percoll–Mg2+ carboxysome enrichment technique using the freshwater cyanobacterium Synechococcus sp. PCC7942. Both matrix-assisted laser desorption–ionization – time of flight mass spectrometry (MALDI-TOF MS) and multidimensional protein identification technology (MuDPIT) methods were used to determine the protein content of a novel carboxysome-rich fraction. A total of 17 proteins were identified using MALDI-TOF MS from enriched carboxysome preparations, while 122 proteins were identified using MuDPIT analysis on the same material. The carboxysomal protein CcmM was identified by MALDI-TOF MS as two distinct proteins of 38 and 58 kDa. The only other carboxysomal proteins identified were the large and small subunits of Rubisco (RbcL and RbcS). Reasons for the lack of evidence for the expected full complement of carboxysomal proteins and future directions are discussed.Key words: CO2-concentrating mechanism, cyanobacteria, carboxysomes, proteomics.

scholarly journals Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

2006 ◽  
Vol 72 (9) ◽  
pp. 6299-6315 ◽  
Author(s):  
Martin G. Klotz ◽  
Daniel J. Arp ◽  
Patrick S. G. Chain ◽  
Amal F. El-Sheikh ◽  
Loren J. Hauser ◽  
...  
Keyword(s):  
Tricarboxylic Acid Cycle ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Type I ◽  
Circular Chromosome ◽  
Bisphosphate Carboxylase ◽  
Terminal Electron Acceptor ◽  
Genes Encoding ◽  
Pentose Phosphate Pathways ◽  
Ammonia Oxidizing Bacterium

ABSTRACT The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

Purification, Characterization and Thermostability of Ribulose 1,5-Bisphosphate Carboxylase-Oxygenase from Barley Leaves

2000 ◽  
Vol 55 (7-8) ◽  
pp. 611-619 ◽  
Author(s):  
Pavlina Dolashka-Angelova ◽  
Syed Abid Ali ◽  
Klimentina Demirevska-Kepova ◽  
Stanka Stoeva ◽  
Wolfgang Voelter
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Structural Integrity ◽  
Higher Plants ◽  
Large Subunit ◽  
Functional Adaptation ◽  
Type I ◽  
Hordeum Vulgare L ◽  
Bisphosphate Carboxylase

Abstract The enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (rubisco) and its functional subunits from barley (Hordeum vulgare L.) leaves were purified to homogeneity by activitydirected sequencial steps of chromatography. Based on the molecular mass estimation by SDS-PAGE, the large subunit (LS) had an apparent molecular weight of ca. 55 kDa, whereas the small subunit (SS) was ca. a 14 kDa polypeptide chain. The N-terminal sequences, established by automated Edman degradation analysis of the purified subunits, showed very close sequence homologies (52-92%) with the subunits of other rubisco enzymes reported from several photosynthetic species. In order to establish the chemical heterogeneity in the rubisco from barley, the amino acid composition of purified native enzyme was analyzed and the results systematically compared with other known type-I rubisco enzymes from spinach, maize, tobacco and pea. Major differences have been observed in the amino acid composition of barley rubisco, the concentration of cysteine, serine, threonine, isoleucine, leucine, arginine and tryptophan residues were found quite variable as compared to other higher plants. The thermostability of the native rubisco was also investigated using circular dichroism and fluorescence spectroscopy. The critical ( Tc) and melting ( Tm) temperatures were determined to be 60 °C and 57 °C, respectively, and at this temperature the enzyme not only retains its structural integrity but also its enzymatic activity. Results of these studies were discussed in the light of structural and functional adaptation of this bifunctional enzvme in C3 and C4 plants to their environments.

Carbon isotope fractionation by photosynthetic aquatic microorganisms: experiments with Synechococcus PCC7942, and a simple carbon flux model

1998 ◽  
Vol 76 (6) ◽  
pp. 1109-1118 ◽  
Author(s):  
Jonathan Erez ◽  
Anne Bouevitch ◽  
Aaron Kaplan
Keyword(s):  
Carbon Isotope ◽  
Carbon Isotopes ◽  
Isotope Fractionation ◽  
Isotopic Fractionation ◽  
Bisphosphate Carboxylase ◽  
Carbon Isotope Fractionation ◽  
Concentrating Mechanism ◽  
Aquatic Microorganisms ◽  
Synechococcus Pcc7942 ◽  
Flux Model

Stable carbon isotopes (12C and 13C) are widely used to trace biogeochemical processes in the global carbon cycle. Natural fractionation of carbon isotopes is mainly due to the discrimination of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) against 13C during photosynthesis. In marine and other aquatic microorganisms, this fractionation is lowered when the dissolved CO2 (CO2(aq)) is decreasing, but the underlying mechanisms are poorly understood. Cultured Synechococcus PCC7942 showed maximum isotopic fractionations of -33omicron (in delta 13C units) relative to the total inorganic carbon (Ci) when CO2(aq) is above 30 m M. As the culture grew, pH increased, CO2(aq) was lower than 1 m M, and the Ci concentrating mechanism was induced although the Ci was above 3 mM. The isotopic fractionation was drastically reduced to values of -1 to -3 omicron relative to Ci. A simple carbon isotope flux model suggests that during the first stages of the experiment the total uptake (F1) was roughly three- to four-fold greater than the photosynthetic net accumulation (F2). When the Ci concentrating mechanism was induced, the leakage of CO2 from the cells declined, the cells started to utilize HCO3- and the F1/F2 ratio decreased to values close to 1. Based on this model the isotopic variability of oceanic phytoplankton suggests that the F1/F2 ratio may be above 3 in high latitudes and ~1.1 in equatorial waters, where the Ci concentrating mechanism is probably induced. Attempts to reconstruct past atmospheric CO2 levels and paleoproductivity should take into account the effects of the Ci concentrating mechanism on the isotopic fractionation of aquatic primary producers.Key words: carbon concentrating mechanism, carbon isotope fractionation, CO2, photosynthesis.

Sign in / Sign up

Export Citation Format

Share Document