Diversity of Betaproteobacteria revealed by novel primers suggests their role in arsenic cycling.

High arsenic concentration in groundwater is a severe environmental problem affecting human health, particularly in countries of South and South-East Asia. The Bengal Delta Plain (BDP) distributed within India and Bangladesh is a major arsenic-affected region where groundwater is the primary source of drinking water. Previous studies have indicated that members of the bacterial class constitute a major fraction of the microbial community in many of the aquifers within this region.

Mechanism of ribosome assisted protein folding: a new insight into rRNA functions.

The peptidyl transferase center (PTC), present in the domain V of 23S rRNA of bacteria can act as a general protein folding modulator. Any general function of a nucleic acid polymer (DNA or RNA) is always related to specific sequence/sequences. The ribosome mediated protein folding also involves a specific interaction between the nucleotides of peptidyl transferase center and the amino acids of an unfolded protein.

Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme.

In vitro protein folding by E. coli ribosome: unfolded protein splitting 70S to interact with 50S subunit.

Folding of unfolded protein on Escherichia coli 70S ribosome is accompanied by rapid dissociation of the ribosome into 50S and 30S subunits. The dissociation rate of 70S ribosome with unfolded protein is much faster than that caused by combined effect of translation and polypeptide release factors known to be involved in the dissociation of ribosome into subunits. The protein then reaches a "folding competent" state on 50S and is released to take up native conformation by itself.

Protein folding following synthesis in vitro and in vivo: association of newly synthesized protein with 50S subunit of E. coli ribosome.

In the accompanying paper, it was shown that a protein, while reverting to native form from the unfolded state in vitro with the help of bacterial 70S ribosome, split the latter into its subunits (50S and 30S) and remains associated with the 50S subunit. Here, we follow the fate of nascent proteins both in case of in vivo and in vitro translation system. The newly synthesised protein was found to associate with the 50S subunit in both the cases.

Ribosome-DnaK interactions in relation to protein folding.

Bacterial ribosomes or their 50S subunit can refold many unfolded proteins. The folding activity resides in domain V of 23S RNA of the 50S subunit. Here we show that ribosomes can also refold a denatured chaperone, DnaK, in vitro, and the activity may apply in the folding of nascent DnaK polypeptides in vivo.

23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding.

The role of the 50S particle of Escherichia coli ribosome and its 23S rRNA in the refolding and subunit association of dimeric porcine heart cytoplasmic malate dehydrogenase (s-MDH) has been investigated. The self-reconstitution of s-MDH is governed by two parallel pathways representing the folding of the inactive monomeric and the dimeric intermediates. However, in the presence of these folding modulators, only one first order kinetics was observed.

Mutations in domain V of the 23S ribosomal RNA of Bacillus subtilis that inactivate its protein folding property in vitro.

The active site of a protein folding reaction is in domain V of the 23S rRNA in the bacterial ribosome and its homologs in other organisms. This domain has long been known as the peptidyl transferase center. Domain V of Bacillus subtilis is split into two segments, the more conserved large peptidyl transferase loop (RNA1) and the rest (RNA2).