scholarly journals Characterization of Genes Responsible for the CO-Linked Hydrogen Production Pathway in Rubrivivax gelatinosus

2010 ◽  
Vol 76 (11) ◽  
pp. 3715-3722 ◽  
Author(s):  
Gary Vanzin ◽  
Jianping Yu ◽  
Sharon Smolinski ◽  
Vekalet Tek ◽  
Grant Pennington ◽  
...  
Keyword(s):  
Large Subunit ◽  
Photosynthetic Bacterium ◽  
Small Subunit ◽  
Proton Pumping ◽  
Amino Acid Sequences ◽  
Membrane Bound ◽  
Rubrivivax Gelatinosus ◽  
Conserved Region ◽  
Energy Converting

ABSTRACT Upon exposure to carbon monoxide, the purple nonsulfur photosynthetic bacterium Rubrivivax gelatinosus produces hydrogen concomitantly with the oxidation of CO according to the equation CO + H2O ↔ CO2 + H2. Yet little is known about the genetic elements encoding this reaction in this organism. In the present study, we use transposon mutagenesis and functional complementation to uncover three clustered genes, cooL, cooX, and cooH, in Rubrivivax gelatinosus putatively encoding part of a membrane-bound, multisubunit NiFe-hydrogenase. We present the complete amino acid sequences for the large catalytic subunit and its electron-relaying small subunit, encoded by cooH and cooL, respectively. Sequence alignment reveals a conserved region in the large subunit coordinating a binuclear [NiFe] center and a conserved region in the small subunit coordinating a [4Fe-4S] cluster. Protein purification experiments show that a protein fraction of 58 kDa molecular mass could function in H2 evolution mediated by reduced methyl viologen. Western blotting experiments show that the two hydrogenase subunits are detectable and accumulate only when cells are exposed to CO. The cooX gene encodes a putative Fe-S protein mediating electron transfer to the hydrogenase small subunit. We conclude that these three Rubrivivax proteins encompass part of a membrane-bound, multisubunit NiFe-hydrogenase belonging to the energy-converting hydrogenase (Ech) type, which has been found among diverse microbes with a common feature in coupling H2 production with proton pumping for energy generation.

Theileria parva ribosomal internal transcribed spacer sequences exhibit extensive polymorphism and mosaic evolution: application to the characterization of parasites from cattle and buffalo

Parasitology ◽  
1999 ◽  
Vol 118 (6) ◽  
pp. 541-551 ◽  
Author(s):  
N. E. COLLINS ◽  
B. A. ALLSOPP
Keyword(s):  
Genetic Recombination ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Gene Pools ◽  
Theileria Parva ◽  
Causative Agents ◽  
Internal Transcribed Spacer Sequences

We sequenced the rRNA genes and internal transcribed spacers (ITS) of several Theileria parva isolates in an attempt to distinguish between the causative agents of East coast fever and Corridor disease. The small subunit (SSU) and large subunit (LSU) rRNA genes from a cloned T. p. lawrencei parasite were sequenced; the former was identical to that of T. p. parva Muguga, and there were minor heterogeneities in the latter. The 5·8S gene sequences of 11 T. parva isolates were identical, but major differences were found in the ITS. Six characterization oligonucleotides were designed to hybridize within the variable ITS1 region; 93·5% of T. p. parva isolates examined were detected by probe TPP1 and 81·8% of T. p. lawrencei isolates were detected by TPL2 and/or TPL3a. There was no absolute distinction between T. p. parva and T. p. lawrencei and the former hybridized with fewer of the probes than did the latter. It therefore seems that a relatively homogenous subpopulation of T. parva has been selected in cattle from a more diverse gene pool in buffalo. The ITSs of both T. p. parva and T. p. lawrencei contained different combinations of identifiable sequence segments, resulting in a mosaic of segments in any one isolate, suggesting that the two populations undergo genetic recombination and that their gene pools are not completely separate.

The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate carboxylase. I. Patterns of variability

1983 ◽  
Vol 31 (4) ◽  
pp. 395 ◽  
Author(s):  
PG Martin ◽  
AC Jennings
Keyword(s):  
Amino Acids ◽  
Large Subunit ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Protein Sequencing ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny ◽  
Variable Site ◽  
N Terminus

Ribulose bisphosphate carboxylase has been prepared from 50 species of angiosperms from 16 diverse families. In 35 preparations, well known 'bland leaf' methods were used but 15 species had 'pungent leaves' and for these a new preparative method is described. Automatic methods have been used to obtain N-terminal sequences (40 amino acids) of the small subunit (SSU) from all 50 species and the pattern of variability is discussed: 26 of 40 positions are variable to a degree similar to that found in plastocyanin and plant cytochrome c, i.e, an average of 3.7 different amino acids per variable site. These results, and the fact that sufficient protein can be obtained from 100 g of leaves, make a widespread phylogenetic survey of angiosperm SSU feasible and it is claimed that the method is at least as practicable as nucleic acid sequencing. A limited amount of sequencing has been carried out on the large subunit (LSU) but its low variability discourages a protein sequencing survey. Implications for gene structure and function are discussed and evidence is given that active LSU is derived from a precursor with 14 additional amino acids at the N-terminus. In SSU, variability of the two N- terminal amino acids suggests that they are not involved in the signals for removal of either the transit peptide or, in the RNA, of the intron, excision of one end of which depends on the codons for the invariable amino acids at positions 3 and 4. Evidence is also given that if the N-terminus of SSU is methionine, as is common, then it is modified and associated with a 'frayed' N-terminus.

scholarly journals The “Green” Form I Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from the Nonsulfur Purple BacteriumRhodobacter capsulatus

1999 ◽  
Vol 181 (13) ◽  
pp. 3935-3941 ◽  
Author(s):  
Kempton M. Horken ◽  
F. Robert Tabita
Keyword(s):  
Genetic Manipulation ◽  
Sequence Similarity ◽  
Large Subunit ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Kinetic Properties ◽  
Phylogenetic Groups ◽  
Bisphosphate Carboxylase ◽  
Related Organism ◽  
Green Form

ABSTRACT Form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) of the Calvin-Benson-Bassham cycle may be divided into two broad phylogenetic groups, referred to as red-like and green-like, based on deduced large subunit amino acid sequences. Unlike the form I enzyme from the closely related organism Rhodobacter sphaeroides, the form I RubisCO from R. capsulatus is a member of the green-like group and closely resembles the enzyme from certain chemoautotrophic proteobacteria and cyanobacteria. As the enzymatic properties of this type of RubisCO have not been well studied in a system that offers facile genetic manipulation, we purified theR. capsulatus form I enzyme and determined its basic kinetic properties. The enzyme exhibited an extremely low substrate specificity factor, which is congruent with its previously determined sequence similarity to form I enzymes from chemoautotrophs and cyanobacteria. The enzymological results reported here are thus strongly supportive of the previously suggested horizontal gene transfer that most likely occurred between a green-like RubisCO-containing bacterium and a predecessor to R. capsulatus. Expression results from hybrid and chimeric enzyme plasmid constructs, made with large and small subunit genes fromR. capsulatus and R. sphaeroides, also supported the unrelatedness of these two enzymes and were consistent with the recently proposed phylogenetic placement of R. capsulatus form I RubisCO. The R. capsulatus form I enzyme was found to be subject to a time-dependent fallover in activity and possessed a high affinity for CO2, unlike the closely similar cyanobacterial RubisCO, which does not exhibit fallover and possesses an extremely low affinity for CO2. These latter results suggest definite approaches to elucidate the molecular basis for fallover and CO2 affinity.

Molecular evolutionary analyses of the small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase

1992 ◽  
Vol 70 (4) ◽  
pp. 715-723 ◽  
Author(s):  
J. J. Pasternak ◽  
B. R. Glick
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Large Subunit ◽  
Distance Matrix ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Bisphosphate Carboxylase ◽  
Tree Building ◽  
Building Methods

The molecular evolution of the amino acid sequences of the mature small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygense (Rubisco) was determined. The dataset for each subunit consisted of sequences from 39 different taxa of which 22 are represented with sequence information for both subunits. Phylogenetic trees were reconstructed using distance matrix, parsimony and simultaneous alignment and phylogeny methods. For the small subunit, the latter two methods produced similar trees that differed from the topology of the distance matrix tree. For the large subunit, each of the three tree-building methods yielded a distinct tree. Except for the distance matrix small subunit tree, the tree-building methods produced topologies for the small and large subunit sequences from the nonflowering plant taxa that, for the most part, agree with current taxonomic schemes. With the full datasets, the lack of consistency both among the various trees and with conventional taxonomic relationships was most evident with the Rubisco sequences from angiosperms. It is unlikely that current tree-building methods will be able to reconstruct an unambiguous molecular evolution of either of the Rubisco subunits. Molecular trees, regardless of methodology, showed similar topologies for the small and large subunits from the 22 taxa from which both subunits have been sequenced, indicating that the subunits have changed to the same extent over time. In this case, similar trees were formed because only 4 of the 22 taxa were from dicots. Key words: ribulose-1,5-bisphosphate carboxylase/oxygenase, amino acid sequence, molecular evolution, phyletic trees.

scholarly journals Identification and Characterization of the Rhizobium sp. Strain GIN611 Glycoside Oxidoreductase Resulting in the Deglycosylation of Ginsenosides

2011 ◽  
Vol 78 (1) ◽  
pp. 242-249 ◽  
Author(s):  
Eun-Mi Kim ◽  
Juhan Kim ◽  
Joo-Hyun Seo ◽  
Jun-Seong Park ◽  
Duck-Hee Kim ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Large Subunit ◽  
Small Subunit ◽  
Compound K ◽  
Oxidation Activity ◽  
Content Type ◽  
Molecular Masses ◽  
Ginsenoside Compound K ◽  
Identification And Characterization

ABSTRACTUsing enrichment culture,Rhizobiumsp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex fromRhizobiumsp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosylation of compound K was performed via oxidation of ginsenoside glucose by glycoside oxidoreductase. Coexpression of the small subunit helped soluble expression of the large subunit in recombinantEscherichia coli. The purified large subunit also showed oxidation activity against other ginsenoside compounds, such as Rb1, Rb2, Rb3, Rc, F2, CK, Rh2, Re, F1, and the isoflavone daidzin, but at a much lower rate. When oxidized CK was extracted and incubated in phosphate buffer with or without enzyme, (S)-protopanaxadiol [PPD(S)] was detected in both cases, which suggests that deglycosylation of oxidized glucose is spontaneous.

scholarly journals Isolation and Characterization of a Novel Facultative Anaerobic Filamentous Fungus from Japanese Rice Field Soil

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Akio Tonouchi
Keyword(s):  
Filamentous Fungus ◽  
Rice Field ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Field Soil ◽  
Rice Field Soil ◽  
Rdna Sequences ◽  
Isolation And Characterization

A novel filamentous fungus strain designated RB-1 was isolated into pure culture from Japanese rice field soil through an anaerobic role tube technique. The strain is a mitosporic fungus that grows in both aerobic and strict anaerobic conditions using various mono-, di-, tri-, and polysaccharides with acetate and ethanol productions. The amount of acetate produced was higher than that of ethanol in both aerobic and anaerobic cultures. The characteristic verrucose or punctuate conidia of RB-1 closely resembled those of some strains of the genusThermomyces, a thermophilic or mesophilic anamorphic ascomycete. However, based on phylogenetic analysis with the small subunit (SSU) and large subunit (LSU) rDNA sequences, RB-1 was characterized as a member of the class Lecanoromycetes of the phylum Ascomycota. Currently, RB-1 is designated as an anamorphic ascomycete and is phylogenetically considered anincertae sediswithin the class Lecanoromycetes.

Peptide composition and enzyme activities of isolated pyrenoids from the green alga Bryopsis maxima

1991 ◽  
Vol 69 (5) ◽  
pp. 1053-1061 ◽  
Author(s):  
M. Okada ◽  
Y. Okabe ◽  
M. Kono ◽  
K. Nakayama ◽  
H. Satoh
Keyword(s):  
Large Subunit ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Starch Synthase ◽  
Minor Components ◽  
Terminal Sequence ◽  
Bisphosphate Carboxylase ◽  
Dna Library ◽  
Peptide Composition ◽  
Bryopsis Maxima

Pyrenoids of Bryopsis maxima contained several minor components other than the large subunit (LS) and the small subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). Among the minor components, polypeptides of 95, 67, and 41 kDa reacted with an antibody against the LS polypeptide. Amino acid sequences of these polypeptides were determined and compared with that deduced from the LS gene (rbcL) screened from the chloroplast DNA library of B. maxima. The N-terminal sequence of the LS peptide was not post-translationally processed and was almost identical with those of the polypeptides of 91, 67, and 41 kDa. The starch grains surrounding the pyrenoids contained a polypeptide of 66 kDa that was assigned as starch synthase. Key words: Bryopsis maxima, nitrate reductase, pyrenoid, rbcL, Rubisco, starch synthase.

scholarly journals Characterization of ADG1, an Arabidopsis locus encoding for ADPG pyrophosphorylase small subunit, demonstrates that the presence of the small subunit is required for large subunit stability

2002 ◽  
Vol 13 (1) ◽  
pp. 63-70 ◽  
Author(s):  
Shue-mei Wang ◽  
Wei-ling Lue ◽  
Tien-shin Yu ◽  
Jih-hau Long ◽  
Chen-nai Wang ◽  
...  
Keyword(s):  
Large Subunit ◽  
Small Subunit

scholarly journals Identification of the conserved domains of ADP-Glucose Pyrophosphorylase (AGPase) protein in sweetpotato (Ipomoea batatas (L.) Lam.) and its two wild relatives

2021 ◽  
Author(s):  
Hualin Nie ◽  
Sujung Kim ◽  
Hohyun Kim ◽  
Ji-Seong Kim ◽  
Sun-Hyung Kim
Keyword(s):  
Ipomoea Batatas ◽  
Large Subunit ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Terminal Region ◽  
The Other ◽  
Conserved Domains ◽  
Molecular Weights ◽  
Grand Average ◽  
Aliphatic Index

Abstract The conserved domains are defined as recurring units in molecular evolution, which are commonly used to interpret the molecular function and biochemical structure of proteins. The AGPase amino acid sequences of three species from the Ipomoea genus were identified to investigate their physicochemical and biochemical characteristics. The molecular weights (MW), isoelectric point (pI), instability index (II), and grand average of hydropathy (GRAVY) showed considerable differences in each plant. The aliphatic index (AI) values of sweetpotato AGPase proteins were higher in the small subunit than in the large subunit. The AGPase proteins from sweetpotato contain an LbH_G1P_AT_C domain in the C-terminal region and various domains (NTP_transferase, ADP_Glucose_PP, or Glyco_tranf_GTA) in the N-terminal region. On the other hand, most of its two relatives (I. trifida and I. triloba) only contain the NTP_transferase domain in the N-terminal region. These findings suggested that these conserved domains were species specificity and related to the subunit types of AGPase proteins. The study may enable research on the AGPase-related specific characteristics of sweetpotatoes, which do not exist in the other two species, such as starch metabolism and tuberization mechanism.

scholarly journals Unusual Organization of the Genes Coding for HydSL, the Stable [NiFe]Hydrogenase in the Photosynthetic BacteriumThiocapsa roseopersicina BBS

1998 ◽  
Vol 180 (6) ◽  
pp. 1460-1465 ◽  
Author(s):  
Gabor Rakhely ◽  
Annette Colbeau ◽  
Jerome Garin ◽  
Paulette M. Vignais ◽  
Kornel L. Kovacs
Keyword(s):  
Electron Transfer ◽  
Gene Cluster ◽  
Large Subunit ◽  
Photosynthetic Bacterium ◽  
Amino Acid Sequences ◽  
Desulfovibrio Vulgaris ◽  
Hydrogenase Activity ◽  
Intergenic Sequence ◽  
Photosynthetic Membrane ◽  
In Cells

ABSTRACT The characterization of a hyd gene cluster encoding the stable, bidirectional [NiFe]hydrogenase 1 enzyme in Thiocapsa roseopersicina BBS, a purple sulfur photosynthetic bacterium belonging to the family Chromatiaceae, is presented. The heterodimeric hydrogenase 1 had been purified to homogeneity and thoroughly characterized (K. L. Kovacs et al., J. Biol. Chem. 266:947–951, 1991; C. Bagyinka et al., J. Am. Chem. Soc. 115:3567–3585, 1993). As an unusual feature, a 1,979-bp intergenic sequence (IS) separates the structural geneshydS and hydL, which encode the small and the large subunits, respectively. This IS harbors two sequential open reading frames (ORFs) which may code for electron transfer proteins ISP1 and ISP2. ISP1 and ISP2 are homologous to ORF5 and ORF6 in thehmc operon, coding for a transmembrane electron transfer complex in Desulfovibrio vulgaris. Other accessory proteins are not found immediately downstream or upstream of hydSL. A hup gene cluster coding for a typical hydrogen uptake [NiFe]hydrogenase in T. roseopersicina was reported earlier (A. Colbeau et al. Gene 140:25–31, 1994). The deduced amino acid sequences of the two small (hupS andhydS) and large subunit (hupL andhydL) sequences share 46 and 58% identity, respectively. The hup and hyd genes differ in the arrangement of accessory genes, and the genes encoding the two enzymes are located at least 15 kb apart on the chromosome. Both hydrogenases are associated with the photosynthetic membrane. A stable and an unstable hydrogenase activity can be detected in cells grown under nitrogen-fixing conditions; the latter activity is missing in cells supplied with ammonia as the nitrogen source. The apparently constitutive and stable activity corresponds to hydrogenase 1, coded byhydSL, and the inducible and unstable second hydrogenase may be the product of the hup gene cluster.

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