Chapter 29 : Replication of Linear Bacterial Chromosomes: No Longer Going Around in Circles

Alignment of Borrelia telomeres. The nucleotide sequences of the telomeres from linear replicons of the indicated species is shown ( 20 , 21 , 39 , 49 , 50 , 59 , 121 ). Conserved telomeric regions are boxed and shaded. The question marks indicate that DNA sequencing around the hairpin was not performed, so there is some uncertainty as to the exact sequence of the turnaround.

The replication strategy for linear replicons with covalently closed hairpin ends in B. burgdorferi. The arrows labeled L and R indicate the inverted repeats at the left and right ends, respectively. The line bisecting the head-to-head (L′-L) and tail-to-tail (R-R′) telomere junctions in the replication intermediate is an axis of 180° rotational symmetry. The telomere breakage and reunion reaction is referred to as telomere resolution. Reprinted from reference 63 with permission from Elsevier.

Mechanism of action of ResT. (A) In a relaxed or linearized plasmid the telomere junction is presented as lineform DNA with a head-to-head structure for the inverted repeat (thin arrows). The scissile phosphates are noted with black dots and are 6 nucleotides apart on opposite strands, placing them on the same face of the DNA double helix. The shaded ovals represent ResT protomers, and the unshaded portions denote the active site with its putative tyrosine nucleophile (Y). The open arrows indicate the orientation of the ResT protomers. For simplicity, the reaction is drawn with active-site function in cis, although whether catalysis actually occurs in cis or in trans is not yet known. DNA cleavage is effected through nucleophilic attack by an active-site tyrosine residue which makes a covalent intermediate with the DNA through a 3′ phosphotyrosine linkage. The 5′ hydroxyl groups are brought into proximity with the phosphotyrosine linkage for transesterification by a conformational change in the complex or by simple dissociation, with joining of the bottom strand to the top strand to produce the DNA hairpin. (B) In a supercoiled plasmid the telomere junction is presented as cruciform DNA with the inverted repeats in the opposite orientation to that found in the lineform DNA. This structure would block interaction of ResT protomers by reversing their relative orientation. They would also be separated in space on the long arms of the extruded cruciform. Additionally, the cleavage sites are moved far from the strand to which they need to be joined for hairpin formation. Reprinted from reference 63 with permission from Elsevier.

Predicted secondary structure of the 3′ end of the S. lividans chromosome. Roman numerals indicate palindrome numbers. The “rabbit ears” secondary structure of the terminal 119 nt based on autonomous parvovirus ( 30 ) is included for comparison. The hairpin sequences that are homologous to a hairpin of the parvoviral genome are shaded. The putative Pu:Pu sheared pairings are indicated by black dots. Palindromes I′ to VII′ are conserved in most Streptomyces chromosomes. Palindromes VIII0 to X0 are absent from some. Modified from references 13 and 56 .

Four models for terminal patching of Streptomyces linear replicons. The intermediate telomere structure with the 3′ single-stranded overhang, which contains the conserved terminal palindromes (I′ to IV′ are indicated), is shown on the top. The terminal protein (TP) is indicated by the filled circle. New TP is represented by open circles, DNA polymerase is represented by open arrows, and newly synthesized DNA is represented by dashed lines. See the text for details about the models. Modified from reference 26 .