scholarly journals Diversity of Bacterial Photosymbionts in Lubomirskiidae Sponges from Lake Baikal

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Nina V. Kulakova ◽  
Natalia N. Denikina ◽  
Sergei I. Belikov
Keyword(s):  
16S Rrna ◽  
Lake Baikal ◽  
Large Subunit ◽  
Molecular Approach ◽  
Freshwater Sponge ◽  
Phylogenetic Groups ◽  
Bisphosphate Carboxylase ◽  
Sponge Symbionts

Sponges are permanent benthos residents which establish complex associations with a variety of microorganisms that raise interest in the nature of sponge-symbionts interactions. A molecular approach, based on the identification of the 16S rRNA and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit genes, was applied to investigate diversity and phylogeny of bacterial phototrophs associated with four species of Lubomirskiidae in Lake Baikal. The phylogeny inferred from both genes showed three main clusters of Synechococcus associated with Baikalian sponges. One of the clusters belonged to the cosmopolitan Synechococcus rubescens group and the two other were not related to any of the assigned phylogenetic groups but placed as sister clusters to S. rubescens. These results expanded the understanding of freshwater sponge-associated photoautotroph diversity and suggested that the three phylogenetic groups of Synechococcus are common photosynthetic symbionts in Lubomirskiidae sponges.

scholarly journals Occurrence, phylogeny and evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase genes in obligately chemolithoautotrophic sulfur-oxidizing bacteria of the genera Thiomicrospira and Thioalkalimicrobium

Microbiology ◽  
2006 ◽  
Vol 152 (7) ◽  
pp. 2159-2169 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Elizaveta M. Spiridonova ◽  
Ivan A. Berg ◽  
Boris B. Kuznetsov ◽  
Dimitry Yu. Sorokin
Keyword(s):  
16S Rrna ◽  
Large Subunit ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Phylogenetic Cluster ◽  
New Family ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Sulfur Oxidizing ◽  
Phylogeny And Evolution

The occurrence of the different genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin–Benson–Bassham cycle of autotrophic CO2 fixation, was investigated in the members of the genus Thiomicrospira and the relative genus Thioalkalimicrobium, all obligately chemolithoautotrophic sulfur-oxidizing Gammaproteobacteria. The cbbL gene encoding the ‘green-like’ form I RubisCO large subunit was found in all analysed species, while the cbbM gene encoding form II RubisCO was present only in Thiomicrospira species. Furthermore, species belonging to the Thiomicrospira crunogena 16S rRNA-based phylogenetic cluster also possessed two genes of green-like form I RubisCO, cbbL-1 and cbbL-2. Both 16S-rRNA- and cbbL-based phylogenies of the Thiomicrospira–Thioalkalimicrobium–Hydrogenovibrio group were congruent, thus supporting its monophyletic origin. On the other hand, it also supports the necessity for taxonomy reorganization of this group into a new family with four genera.

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.

scholarly journals Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2387-2398 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Elizaveta M. Spiridonova ◽  
Ivan A. Berg ◽  
Natalia V. Slobodova ◽  
Eugenia S. Boulygina ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Large Subunit ◽  
Nifh Gene ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Bisphosphate Carboxylase ◽  
Purple Sulfur Bacterium ◽  
The Family

The occurrence of genes encoding nitrogenase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) was investigated in the members of the family Ectothiorhodospiraceae. This family forms a separate phylogenetic lineage within the Gammaproteobacteria according to 16S rRNA gene sequence analysis and mostly includes photo- and chemoautotrophic halophilic and haloalkaliphilic bacteria. The cbbL gene encoding the large subunit of ‘green-like’ form I RubisCO was found in all strains, except the type strains of Alkalispirillum mobile and Arhodomonas aquaeolei. The nifH gene encoding nitrogenase reductase was present in all investigated species of the phototrophic genera Ectothiorhodospira, Halorhodospira and Thiorhodospira, but not of the genus Ectothiorhodosinus. Unexpectedly, nifH fragments were also obtained for the chemotrophic species Thioalkalispira microaerophila and Alkalilimnicola halodurans, for which diazotrophic potential has not previously been assumed. The cbbL-, nifH- and 16S rRNA gene-based trees were not highly congruent in their branching patterns since, in the ‘RubisCO’ and ‘nitrogenase’ trees, representatives of the Ectothiorhodospiraceae are divided in a number of broadly distributed clusters and branches. However, the data obtained may be regarded as evidence of the monophyletic origin of the cbbL and nifH genes in most species within the family Ectothiorhodospiraceae and mainly corresponded to the current taxonomic structure of this family. The cbbL phylogeny of the chemolithoautotrophic sulfur-oxidizers Thioalkalivibrio nitratireducens and Thioalkalivibrio paradoxus and the nitrifier Nitrococcus mobilis deviated significantly from the 16S-rRNA gene-based phylogeny. These species clustered with one of the duplicated cbbL genes of the purple sulfur bacterium Allochromatium vinosum, a member of the family Chromatiaceae.

scholarly journals Diversity of Green-Like and Red-Like Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes (cbbL) in Differently Managed Agricultural Soils

2005 ◽  
Vol 71 (1) ◽  
pp. 175-184 ◽  
Author(s):  
Draženka Selesi ◽  
Michael Schmid ◽  
Anton Hartmann
Keyword(s):  
Agricultural Soils ◽  
Large Subunit ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Bacterial Isolates ◽  
Phylogenetic Groups ◽  
Bisphosphate Carboxylase ◽  
Pcr Products ◽  
High Level

ABSTRACT A PCR-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I large-subunit genes (cbbL) as a functional marker of autotrophic bacteria that fix carbon dioxide via the Calvin-Benson-Bassham cycle. We constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbL genes. The diversity of these cbbL genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. cbbL gene fragments were amplified from extracted soil DNAs, and PCR products were cloned and screened by restriction fragment length polymorphism analysis. Selected unique cbbL clones were sequenced and analyzed phylogenetically. The green-like cbbL sequences revealed a very low level of diversity, being closely related to the cbbL genes of Nitrobacter winogradskyi and Nitrobacter vulgaris. In contrast, the red-like cbbL gene libraries revealed a high level of diversity in the two fertilized soils and less diversity in unfertilized soil. The majority of environmental red-like cbbL genes were only distantly related to already known cbbL sequences and even formed separate clusters. In order to extend the database of available red-like cbbL sequences, we amplified cbbL sequences from bacterial type culture strains and from bacterial isolates obtained from the investigated soils. Bacterial isolates harboring the cbbL gene were analyzed phylogenetically on the basis of their 16S rRNA gene sequences. These analyses revealed that bacterial genera such as Bacillus, Streptomyces, and Arthrobacter harbor red-like cbbL genes which fall into the cbbL gene clusters retrieved from the investigated soils.

scholarly journals A distinct assembly pathway of the human 39S late pre-mitoribosome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jingdong Cheng ◽  
Otto Berninghausen ◽  
Roland Beckmann
Keyword(s):  
16S Rrna ◽  
Affinity Purification ◽  
Large Subunit ◽  
Assembly Pathway ◽  
Assembly Factors ◽  
Peptidyltransferase Center

AbstractAssembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.

Phylogeny of the Australian freshwater crayfish Cherax destructor-complex (Decapoda : Parastacidae) inferred from four mitochondrial gene regions

2005 ◽  
Vol 19 (3) ◽  
pp. 209 ◽  
Author(s):  
Thuy T. T. Nguyen ◽  
Christopher M. Austin
Keyword(s):  
16S Rrna ◽  
Cytochrome Oxidase ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
Strong Support ◽  
Interspecific Variation ◽  
Rrna Gene ◽  
Freshwater Crayfish ◽  
Cherax Destructor ◽  
Australian Freshwater

The phylogenetic relationships among 32 individuals of Australian freshwater crayfish belonging to the Cherax destructor-complex were investigated using a dataset comprising sequences from four mitochondrial gene regions: the large subunit rRNA (16S rRNA), cytochrome oxidase I (COI), adenosine triphosphatase 6 (ATPase 6), and cytochrome oxidase III (COIII). A total of 1602 bp was obtained, and a combined analysis of the data produced a tree with strong support (bootstrap values 94–100%) for three divergent lineages, verifying the phylogenetic hypotheses of relationships within the C. destructor species-complex suggested in previous studies. Overall, sequences from the 16S rRNA gene showed the least variation compared to those generated from protein coding genes, which presented considerably greater levels of divergence. The level of divergence within C. destructor was found to be greater than that observed in other species of freshwater crayfish, but interspecific variation among species examined in the present study was similar to that reported previously.

scholarly journals Characterization of the gene and mRNA of the large subunit of ribulose-1,5-bisphosphate carboxylase in pea plants.

1983 ◽  
Vol 3 (4) ◽  
pp. 587-595 ◽  
Author(s):  
K K Oishi ◽  
K K Tewari
Keyword(s):  
Immunoglobulin G ◽  
Large Subunit ◽  
Rrna Genes ◽  
Mapping Technique ◽  
Affinity Column ◽  
Bisphosphate Carboxylase ◽  
Bamhi Fragment ◽  
Dna Fragment

mRNA coding for the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase was obtained by fractionating chloroplast polysomes on an affinity column, using anti-ribulose-1,5-bisphosphate carboxylase immunoglobulin G. Approximately 20% of the polysomal RNA specifically bound to the affinity column. LS mRNA was also isolated by fractionating chloroplast polysomal RNA on sucrose gradients. The LS mRNA fraction was identified by translation in vitro followed by immunoprecipitation with anti-ribulose-1,5-bisphosphate carboxylase immunoglobulin G. Labeled LS mRNA was hybridized to a genomic digests of pea chloroplast DNA. The LS gene was localized on a 3.55-kilobase pair BamHI fragment in SalI-SmaI DNA fragment 4. The BamHI fragment containing the LS gene was cloned, and a restriction endonuclease map was constructed. The LS gene was localized on a 1.9-kbp KpnI-EcoRI fragment. The LS gene was analyzed by electron microscopy, using the R loop mapping technique. LS mRNA was colinear with the gene, and its size was 1.35 +/- 0.2 kilobase pairs. When the LS mRNA was analyzed on methylmercury agarose gels, it comigrated with the 16S rRNA. The direction of transcription of the LS gene was in the same direction as that of the rRNA genes.

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