scholarly journals Diel Rhythms in Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase and Glutamine Synthetase Gene Expression in a Natural Population of Marine Picoplanktonic Cyanobacteria (Synechococcusspp.)

1999 ◽  
Vol 65 (8) ◽  
pp. 3651-3659 ◽  
Author(s):  
Michael Wyman
Keyword(s):  
Glutamine Synthetase ◽  
Natural Population ◽  
Nitrogen Assimilation ◽  
Large Subunit ◽  
Natural Populations ◽  
Carbon Assimilation ◽  
Ribulose Bisphosphate Carboxylase ◽  
Temporal Separation ◽  
Bisphosphate Carboxylase ◽  
Carbon And Nitrogen

ABSTRACT Diel periodicity in the expression of key genes involved in carbon and nitrogen assimilation in marine Synechococcus spp. was investigated in a natural population growing in the surface waters of a cyclonic eddy in the northeast Atlantic Ocean.Synechococcus sp. cell concentrations within the upper mixed layer showed a net increase of three- to fourfold during the course of the experiment (13 to 22 July 1991), the population undergoing approximately one synchronous division per day. Consistent with the observed temporal pattern of phycoerythrin (CpeBA) biosynthesis, comparatively little variation was found incpeBA mRNA abundance during either of the diel cycles investigated. In marked contrast, the relative abundance of transcripts originating from the genes encoding the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL) and glutamine synthetase (glnA) showed considerable systematic temporal variation and oscillated during the course of each diel cycle in a reciprocal rhythm. Whereas activation of rbcL transcription was clearly not light dependent, expression of glnAappeared sensitive to endogenous changes in the physiological demands for nitrogen that arise as a natural consequence of temporal periodicity in photosynthetic carbon assimilation. The data presented support the hypothesis that a degree of temporal separation may exist between the most active periods of carbon and nitrogen assimilation in natural populations of marine Synecoccoccus spp.

scholarly journals The perspectives for DNA barcoding of Rhaponticum carthamoides (Willd.) Iljin using rbcL gene sequence

2021 ◽  
Vol 908 (1) ◽  
pp. 012030
Author(s):  
M V Protopopova ◽  
N A Shvetsova ◽  
V V Pavlichenko
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Dna Barcode ◽  
Natural Populations ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Rhaponticum Carthamoides ◽  
South Siberia ◽  
Illegal Harvesting

Abstract The methods of biological species identification using nucleotide sequences of short genome regions (DNA barcoding) are actively developed. The universal DNA barcode for plants remains to be discovered, and one of the leading candidates is the plastid gene of the large subunit of ribulose-bisphosphate carboxylase gene (rbcL). In our study, we estimated the part of rbcL gene as a possible marker for molecular identification of Rhaponticum carthamoides (Willd.) Iljin. Due to its officinal properties, the species is susceptible to uncontrolled and illegal harvesting from natural populations. Today, the species needs to be protected and therefore is included into the Red Data Books of the Russian Federation and certain regions. The study was carried out using plants from the natural populations sampled from the Khamar-Daban Ridge (South Siberia) and considering now as Rh. carthamoides var. chamarense (Peschkova) O S Zhirova. It was shown that rbcL gene can be used to identify Rh. carthamoides at least from the populations of the Khamar-Daban Ridge using a fragment of the maximum length or its 3’ region. Apparently, the 5’ region of the gene (rbcLa) most often used as DNA barcode for plants may be of lesser importance for Rh. carthamoides. The rbcL gene sequences can be also used for the development of approaches for Rh. carthamoides identification in the medicinal preparations and products containing dried tissues to prevent their falsification and illegal harvesting of this species. The combination of rbcL gene with additional markers seems to be highly desirable to create effective DNA barcodes for Rhaponticum species.

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.

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 Land plant biochemistry

2000 ◽  
Vol 355 (1398) ◽  
pp. 833-846 ◽  
Author(s):  
J. A. Raven
Keyword(s):  
Large Subunit ◽  
Molecular Genetic ◽  
Land Plant ◽  
Water Repellent ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Plant Biochemistry ◽  
Ribulose Bisphosphate Carboxylase Oxygenase ◽  
Molecular Phylogenetic ◽  
Molecular Genetic Evidence

Biochemical studies have complemented ultrastructural and, subsequently, molecular genetic evidence consistent with the Charophyceae being the closest extant algal relatives of the embryophytes. Among the genes used in such molecular phylogenetic studies is that ( rbcL ) for the large subunit of ribulose bisphosphate carboxylase–oxygenase (RUBISCO). The RUBISCO of the embryophytes is derived, via the Chlorophyta, from that of the cyanobacteria. This clade of the molecular phylogeny of RUBISCO shows a range of kinetic characteristics, especially of CO 2 affinities and of CO 2 / O 2 selectivities. The range of these kinetic values within the bryophytes is no greater than in the rest of the embryophytes; this has implications for the evolution of the embryophytes in the high atmospheric CO 2 environment of the late Lower Palaeozoic. The differences in biochemistry between charophycean algae and embryophytes can to some extent be related functionally to the structure and physiology of embryophytes. Examples of components of embryophytes, which are qualitatively or quantitatively different from those of charophytes, are the water repellent/water resistant extracellular lipids, the rigid phenolic polymers functional in waterconducting elements and mechanical support in air, and in UV–B absorption, flavonoid phenolics involved in UV–B absorption and in interactions with other organisms, and the greater emphasis on low M r organic acids, retained in the plant as free acids or salts, or secreted to the rhizosphere. The roles of these components are discussed in relation to the environmental conditions at the time of evolution of the terrestrial embryophytes. A significant point about embryophytes is the predominance of nitrogen–free extracellular structural material (a trait shared by most algae) and UV–B screening components, by contrast with analogous components in many other organisms. An important question, which has thus far been incompletely addressed, is the extent to which the absence from bryophytes of the biochemical pathways which produce components found only in tracheophytes is the result of evolutionary loss of these functions.

scholarly journals Effect of mutation of lysine-128 of the large subunit of ribulose bisphosphate carboxylase/oxygenase from Anacystis nidulans

1998 ◽  
Vol 336 (2) ◽  
pp. 387-393 ◽  
Author(s):  
Graeme BAINBRIDGE ◽  
P. John ANRALOJC ◽  
Pippa J. MADGWICK ◽  
Jim E. PITTS ◽  
Martin A. J. PARRY
Keyword(s):  
Aspartic Acid ◽  
Active Site ◽  
Large Subunit ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Catalytic Function ◽  
Loop Dynamics ◽  
Ribulose Bisphosphate Carboxylase Oxygenase ◽  
Genes Encoding ◽  
Specificity Factor

The contribution of lysine-128 within the active site of Anacystis nidulansd-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) was investigated by the characterization of mutants in which lysine-128 was replaced with arginine, glycine, glutamine, histidine or aspartic acid. Mutated genes encoding the Rubisco large subunit were expressed in Escherichia coliand the resultant polypeptides assembled into active complexes. All of the mutant enzymes had a lower affinity for ribulose 1,5-bisphosphate (RuBP) and lower rates of carboxylation. Substitution of lysine-128 with glutamine, histidine or aspartic acid decreased the specificity factor and led to the production of an additional monophosphate reaction product. We show that this product results from the loss of the phosphate from C-1 of RuBP, most probably by β-elimination from the 2,3-enediolate derivative of RuBP. The results confirm that lysine-128 is important in determining the position of the essential ε-amino group of lysine-334 within the active site and in loop dynamics. This further demonstrates that residues remote from the active site can be manipulated to modify catalytic function.

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