First, direct isolation and analysis of the end of the linear chromosome with its covalently attached terminal protein by biochemical means is definitive (Lin et al., 1993; Goshi et al., 2002). Secondly, an analysis of the gene topology by pulsed-field gel electrophoresis (PFGE) is highly suggestive (Rednenbach et al., 2000). Finally, identification of genes associated with chromosome linearity, such as tpg (gene encoding the terminal protein that is covalently linked to the end of the linear chromosome), tap (gene encoding a telomere-associated protein that seems to be essential to linear chromosome replication

and is usually closely linked with tpg on the chromosome) and ttr (gene encoding a protein U0126 mouse that is present very close to

ends of most linear chromosomes and seems to be involved in linear genome mobilization), implies linearity is present or was present at some point in the past (Goshi et al., 2002; Huang et al., 2007; Suzuki et al., 2008; Kirby & Chen, 2011). However, the absence of homologues of one or all of the tpg, tap and ttr trio does not confirm circularity because there is significant diversity in the terminal Selleck Anti-diabetic Compound Library replication mechanism of linear chromosomes and plasmids of Actinomycetales (Huang et al., 2007; Suzuki et al., 2008). The problems of defining linearity other than by definitive biochemical means, which is laborious, can be illustrated in a number of ways. Using PFGE, Saccharopolyspora erythraea NRRL 2338 was suggested BCKDHA to be linear based on analysis of the absence and presence of chromosome bands before and after proteinase

K treatment (Reeves et al., 1998). However, by chromosome sequencing, Oliynyk et al. (2007) indicated that the chromosome of this species is circular. Analysis at the gene level of the chromosome sequence does not identify any homologues of the tpg, tap and ttr trio or the presence of terminal repeats, which supports the latter conclusion. Notwithstanding the missed restriction sites pinpointed by the chromosome sequencing, the entry of the 8 Mb chromosome into the PFGE gel after proteinase K digestion, and the failure of the untreated chromosome to enter the gel under identical circumstances, supports directly the presence of bound terminal protein at the ends of a linear chromosome. Furthermore, Oliynyk et al. (2007) provide indirect evidence to support circularity, for example on the basis of the detection by gel electrophoresis of a fragment overlapping both proposed termini of the linear chromosome. The question remains somewhat open, but perhaps biased towards circularity. In the case of other Actinomycetales chromosome sequences, there is even less evidence to support circularity.