A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene

Abstract

The dnaK operon from Bacillus subtilis and other Gram-positive bacteria with low G+C DNA content contains additional heat-shock genes, including hrcA. The hrcA gene encodes a transcription factor that negatively regulates heatshock genes and is uniformly present in all Gram-positive bacteria studied to date. An hrcA homologue is also present in Synechocystis species, Leptospira in terrogans, Chlamydia trachoma tis, Cauloba cter crescen tus and Methanococcus jannaschii, organisms that diverged early on f rom the common ancestor of all Gram-positive bacteria and Profeobacteria, according to 165 rRNA phylogeny. A partial, protein-based phylogenetic tree, derived using amino acid sequence homology of hrcA proteins from Gram-positive bacteria, is presented here, and the results are compared with the phylogenetic trees generated from 16s rRNA, dnaK and dnal sequences. The location of the hrcA gene and the genome organization of the dnaK operon support the division of all Gram-positive bacteria into three major groups: one group contains high-G+C Gram-positive bacteria, and two others contain low-G+C Gram-positive bacteria. Among the Gram-positive bacteria with low G+C DNA content, the results indicate that there is a close phylogenetic relationship between Bacillus species and Clostridium species on the one hand and between Lactococcus lactis and Streptococcus mutans on the other. Streptomyces and Mycobacterium species also exhibited a close relationship. A hierarchical arrangement of Gram-positive bacteria based on HrcA sequences is proposed as an additional refinement of the phylogenetic relationships within this important bacterial group.Keywords : hrcA, dnaK operon, Gram-positive bacteria, phylogeny INTRODUCTIONThe evolutionary relationships among microorganisms are being determined by partial or complete sequencing of 5s and 16s rRNA genes (Olsen & Woese, 1993 ;Stackebrandt & Goebel, 1994 ;Stackebrandt et al., 1997;Woese, 1994) mainly because their resistance to evolutionary change allows the entire phylogenetic span of ancient and modern prokaryotes to be analysed simultaneously. However, it has been shown that the resolution power of rRNA sequences Is limited when closely related organisms that diverged at almost the same time are being Falah & Gupta, 1994; Gupta, 1995;Gupta & Golding, 1993;Gupta et a/., 1989). These analyses have revealed a number of important differences relative to rRNA-based phylogenies (Boorstein et al., 1994;Brown et al., 1994;Gupta & Golding, 1993 terial groups that diverged at almost the same time; amino acid sequence homologies, for other proteins that are not so highly conserved, and gene-fusion events may be more appropriate methods (Ahmad & Jensen, 1989; Jensen & Ahmad, 1990). Furthermore, a study based on a very small number of genes could give misleading results if one of the genes had been horizontally transferred across bacterial groups at an earlier stage of divergence. Thus, greater resolution of evolutionary branching can be achieved only by using a greater number of evol...

Evidence for Horizontal Gene Transfer in Evolution of Elongation Factor Tu in Enterococci

“…This is similar to a previous finding based on phylogenetic analysis of the 16S rRNA gene and the hrcA gene coding for a unique heat shock regulatory protein (1). The enterococcal tufA genes branched with most of the low-GϩC-content gram-positive bacteria, suggesting that they originated from a common ancestor.…”

Renaturation of Bacillus thermoglucosidasius HrcA Repressor by DNA and Thermostability of the HrcA-DNA Complex In Vitro

“…Furthermore, in Bradyrhizobium japonicum 110spc4, elevated levels of GroESL in an hrcA mutant had no influence on free-living growth and symbiotic nitrogen fixation (11). The many examples of cooperation between HrcA and these chaperones for proper function of HrcA in diverse bacteria (1) are consistent with the common and stable characteristics that HrcA is hardly soluble and easily forms aggregates when expressed and purified from Escherichia coli. This unfavorable characteristic was reported for B. subtilis HrcA (19), B. stearothermophilus HrcA (12), Staphylococcus aureus HrcA (16), and C. acetobutylicum HrcA (17).…”

Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium.

“…However, the order of branching among Gram-positive bacteria (Firmicutes) on the basis of 16S rRNA sequences has to be interpreted with care. Ahmad et al (1999) have compared three phylogenetic P. P. Bosshard, R. Zbinden and M. Altwegg trees generated from 16S rRNA, DnaK (Hsp70) and DnaJ (Hsp40). They found significant discrepancies in the branching order of the three trees.…”