Characterization of the groEL and groES Loci in Bifidobacterium breve UCC 2003: Genetic, Transcriptional, and Phylogenetic Analyses

Abstract

The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes, including the GroEL and GroES proteins. The groES and groEL genes are highly conserved among eubacteria and are typically arranged as an operon. Genome analysis of Bifidobacterium breve UCC 2003 revealed that the groES and groEL genes are located in different chromosomal regions. The heat inducibility of the groEL and groES genes of B. breve UCC 2003 was verified by slot blot analysis. Northern blot analyses showed that the cspA gene is cotranscribed with the groEL gene, while the groES gene is transcribed as a monocistronic unit. The transcription initiation sites of these two mRNAs were determined by primer extension. Sequence and transcriptional analyses of the region flanking the groEL and groES genes of various bifidobacteria revealed similar groEL-cspA and groES gene units, suggesting a novel genetic organization of these chaperones. Phylogenetic analysis of the available bifidobacterial groES and groEL genes suggested that these genes evolved differently. Discrepancies in the phylogenetic positioning of groES-based trees make this gene an unreliable molecular marker. On the other hand, the bifidobacterial groEL gene sequences can be used as an alternative to current methods for tracing Bifidobacterium species, particularly because they allow a high level of discrimination between closely related species of this genus.

Identification of iron-regulated genes of Bifidobacterium breve UCC2003 as a basis for controlled gene expression

“…Following chelation of ferrous iron, B. breve UCC2003 evokes a stress-like response demonstrated by the upregulation of the chaperone GroEL (Bbr_1364). 38,39 Iron-chelation was also shown to upregulate transcription of nrdF (Bbr_1898), encoding a predicted ribonucleotide reductase. The latter enzyme is known in E. coli to catalyze the reduction of ribonucleotides to deoxyribonucleotides as a first step in the pathway for DNA replication, where synthesis of nrd mRNA increases when DNA synthesis is inhibited.…”

Metascardovia criceti Gen. Nov., Sp. Nov., from Hamster Dental Plaque

“…In recent years, several house keeping genes, such as genes encoding transaldolase, ATPase (atpBEFHAGDC), elongation factor Tu (tuf), and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp), and recombination protein A (recA) have been used for taxonomical studies of bifidobacterial species (15,18,29,30,34). Further, because of their highly conserved primary structures and ubiquity, genes encoding heat shock proteins (HSP60 gene; also known as groEL or cpn60, groES and dnaK genes) were used for detection and identification of microorganisms (5,8,11,25,28,31). Bifidobacterium inopinatum and Bifidobacterium denticolens, isolated from human dental caries, were transferred to S. inopinata and P. denticolens, respectively, according to the taxonomical studies based on HSP60 sequences (10).…”

Genomics ofActinobacteria: Tracing the Evolutionary History of an Ancient Phylum

“…In these trees, actinobacterial species form compact groups, and it has been difficult to solve the precise branching order or interrelationships among different constituent subgroups (406). Thus, other alternative molecular markers such as recA, tuf, atpD, rpoB, sod, gyrB, or molecular chaperoneencoding genes such as groEL, dnaK, grpE, clpP, and hsp65 have been proposed to infer phylogeny in Actinobacteria taxa, such as bifidobacteria (210,(448)(449)(450)(451)(452)(453)(454)(455)(456)(457)(458)(459)(460)(461) or mycobacteria (32,49,149,217,226,497). However, molecular phylogenies based on a single gene often lead to apparently conflicting results (374).…”