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.

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.

Old versus new characters for systematics: Cautionary tales from virology

1990 ◽  
Vol 3 (1) ◽  
pp. 159
Author(s):  
A Gibbs ◽  
A Ding ◽  
J Howe ◽  
P Keese ◽  
A MacKenzie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Recombination ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Molecular Sequence ◽  
Taxonomic Methods ◽  
Cautionary Tales

Molecular sequence information about viruses has mostly confirmed the groupings devised by traditional taxonomic methods, but shown in addition that the genes of related species may differ in number, arrangement, orientation and in sequence homology. It has also revealed that true genetic recombination between viruses has been common, even among those with RNA genomes, indeed most virus groups seem to have arisen y recombination. Thus, there is an unexpected wealth of genetic chaos hidden behind the fatade of the phenotype, and it is possible that the difficulties that plant taxonomists have had in identifying the relationships of the major groupings of plants could have similar causes. Nonetheless, molecular taxonomy does give sensible results and this is illustrated by a classification of the large subunit Rubisco proteins of 21 plant species based on their amino acid sequences.

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.

The Study of Plant Phylogeny Using Amino-Acid-Sequences of Ribulose-1,5-Bisphosphate Carboxylase .VI. Some Solanum and Allied Species From Different Continents

1986 ◽  
Vol 34 (2) ◽  
pp. 187 ◽  
Author(s):  
PG Martin ◽  
JM Dowd ◽  
C Morris ◽  
DE Symon
Keyword(s):  
Amino Acid ◽  
Continental Drift ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Ribulose Bisphosphate Carboxylase ◽  
Ribulose Bisphosphate ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny ◽  
Molecular Evolutionary Clock ◽  
Evolutionary Clock

The N-terminal 40 amino acid sequences of the small subunit of ribulose bisphosphate carboxylase have been determined for 13 species of Solanum, one other species of Solanaceae and two of Convolvulaceae. From these, and previously published sequences from Solanaceae, a minimal phylogenetic tree is derived. This agrees well with current taxonomy; the first dichotomy in the Solanaceae tree is between the two subfamilies Solanoideae and Cestroideae; within Solanum the subgenera Solanum and Leptostemonum separate dichotomously; within subgenus Leptostemonum the African and Asian species diverge from the Australian. Within the Australian species of subgenus Leptostemonum two most unusual substitutions have been noted. The implications for the hypotheses of a 'molecular evolutionary clock' and of biogeographical dispersal by continental drift are discussed.

The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate Carboxylase. V. Magnoliaceae, Polygonaceae and the concept of primitiveness

1984 ◽  
Vol 32 (3) ◽  
pp. 301 ◽  
Author(s):  
PG Martin ◽  
JM Dowd
Keyword(s):  
Amino Acid ◽  
Cytochrome C ◽  
Phylogenetic Tree ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Family Tree ◽  
Ribulose Bisphosphate Carboxylase ◽  
Ribulose Bisphosphate ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny

N-terminal, 40 amino acid sequences of ribulose bisphosphate carboxylase small subunit are given for three species of Polygonaceae, three of Magnoliaceae and for Metasequoia. Making use of three plastocyanin and one cytochrome c sequences from the literature, these families are added to a previously published phylogenetic tree. Fagaceae and Proteaceae are also added. Uncertainties in the 14-family tree are pointed out. The root of the tree is identified using gymnosperm sequences. The concept of primitiveness as it is relevant to this research is discussed. From the phylogenetic tree there is no evidence for primitiveness of Magnoliaceae, though it is not precluded. Polygonaceae and Chenopodiaceae form a branch that diverges from the main tree near the presumptive dicotyledonous origin.

The Study of Plant Phylogeny Using Amino Acid Sequences of Ribulose-1,5-Bisphosphate Carboxylase. IV. Proteaceae and Fagaceae and the Rate of Evolution of the Small Subunit

1984 ◽  
Vol 32 (3) ◽  
pp. 291 ◽  
Author(s):  
PG Martin ◽  
JM Dowd
Keyword(s):  
Amino Acid ◽  
Plate Tectonics ◽  
Phylogenetic Trees ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny ◽  
Rates Of Evolution ◽  
Molecular Evolutionary Clock

N-terminal, 40 amino acid sequences of ribulose bisphosphate carboxylase small subunit (SSU) are given for four species of Proteaceae, six of Fagaceae including four from Nothofagus, and seven from Solanaceae including six new sequences from Nicotiana. Phylogenetic trees, regarded as tentative since only one protein is involved, are given for each of the three groups and approximate positions of the families in the angiosperm tree are indicated. An example of the destabilizing of a hitherto invariant site is given. Working from the 'molecular evolutionary clock' hypothesis, and deriving time from plate tectonics, the data from both Proteaceae and Nothofagus lead to rates of evolution of SSU of one non-silent nucleotide substitution per 9 My. This agrees with an early Cretaceous origin of the angiosperms. A test is proposed to distinguish distributions that are the result of 'vicariance biogeography' from those due to 'dispersal biogeography'. It is concluded that distribution of Nicotiana is most likely due to dispersal.

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.

The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate Carboxylase. III. Addition of Malvaceae and Ranunculaceae to the phylogenetic tree

1984 ◽  
Vol 32 (3) ◽  
pp. 283 ◽  
Author(s):  
PG Martin ◽  
JM Dowd
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Phylogenetic Tree ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Ribulose Bisphosphate Carboxylase ◽  
Ribulose Bisphosphate ◽  
Bisphosphate Carboxylase ◽  
Plant Phylogeny

The N-terminal sequences (40 amino acids) are given for the small subunit (SSU) of ribulose bisphosphate carboxylase from three species of Ranunculaceae and three species of Malvaceae. Methods are given for integrating these into a previously published phylogenetic tree for eight families. The two new familial nodes that have been derived group closely with each other and with equivalent nodes of Asteraceae and Caprifoliaceae. There appears to be considerably more variation in Ranunculaceae than in Malvaceae and possible reasons for this are discussed.

The study of plant phylogeny using amino acid sequences of Ribulose-1,5-Bisphosphate Carboxylase. II. The analysis of small subunit data to form phylognetic trees.

1983 ◽  
Vol 31 (4) ◽  
pp. 411 ◽  
Author(s):  
PG Martin ◽  
JM Dowd ◽  
SJL Stone
Keyword(s):  
Amino Acid ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Ribulose Bisphosphate Carboxylase ◽  
Ribulose Bisphosphate ◽  
Minimal Tree ◽  
Bisphosphate Carboxylase ◽  
Computer Methods ◽  
Plant Phylogeny ◽  
Angiosperm Species

The first 40 amino acid sequences of the small subunit of ribulose bisphosphate carboxylase are given for 24 angiosperm species, three from each of eight families chosen because cytochrome c and plastocyanin sequences are already available. Using computer methods, these data have been analysed to yield minimal phylogenetic Steiner trees. A well defined minimal tree becomes apparent when data from all three proteins are combined. The root of the minimal tree is indicated by the node where a gymnosperm joins. The minimal tree is briefly compared with published phylogenies: in agreement is the divergence of the dicotyledons and monocotyledons from the root and the grouping of the Asteraceae and Caprifoliaceae; in disagreement, and a feature of all three proteins, is the close grouping of the Fabaceae with the Brassicaceae.

scholarly journals NH2-terminal amino acid sequences of precursor and mature forms of the ribulose-1,5-bisphosphate carboxylase small subunit from Chlamydomonas reinhardtii.

1979 ◽  
Vol 83 (3) ◽  
pp. 615-622 ◽  
Author(s):  
G W Schmidt ◽  
A Devillers-Thiery ◽  
H Desruisseaux ◽  
G Blobel ◽  
N H Chua
Keyword(s):  
Amino Acid ◽  
Chlamydomonas Reinhardtii ◽  
Sequence Data ◽  
Cell Extract ◽  
Small Subunit ◽  
Major Product ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Bisphosphate Carboxylase

A precursor (pS) to the small subunit (S) of ribulose1-,5-bisphosphate carboxylase is the major product of cell-free protein synthesis directed by poly(A) containing RNA from Chlamydomonas reinhardtii. We present sequence data for in vitro-synthesized pS, for in vitro-synthesized S that in generated from pS by posttranslational incubation with a Chlamydomonas cell extract, and for in vitro-synthesized, mature S. We show that pS contains an NH2-terminal extension of 44 amino acid residues that is removed by cleavage at the correct site when pS is converted to S by an endoprotease present in the Chlamydomonas cell extract.

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