Xeroderma pigmentosum (XP) is a rare DNA repair disorder characterized by increased susceptibility to UV radiation (UVR)-induced skin pigmentation, skin cancers, ocular surface disease, and, in some patients, sunburn and neurological degeneration. Genetically, it is assigned to eight complementation groups (XP-A to -G and variant). For the last 5 y, the UK national multidisciplinary XP service has provided follow-up for 89 XP patients, representing most of the XP patients in the United Kingdom. Causative mutations, DNA repair levels, and more than 60 clinical variables relating to dermatology, ophthalmology, and neurology have been measured, using scoring systems to categorize disease severity. This deep phenotyping has revealed unanticipated heterogeneity of clinical features, between and within complementation groups. Skin cancer is most common in XP-C, XP-E, and XP-V patients, previously considered to be the milder groups based on cellular analyses. These patients have normal sunburn reactions and are therefore diagnosed later and are less likely to adhere to UVR protection. XP-C patients are specifically hypersensitive to ocular damage, and XP-F and XP-G patients appear to be much less susceptible to skin cancer than other XP groups. Within XP groups, different mutations confer susceptibility or resistance to neurological damage. Our findings on this large cohort of XP patients under long-term follow-up reveal that XP is more heterogeneous than has previously been appreciated. Our data now enable provision of personalized prognostic information and management advice for each XP patient, as well as providing new insights into the functions of the XP proteins.UV radiation | nucleotide excision repair | skin cancer | ocular disease | neurodegeneration

Iron uptake systems which are critical for bacterial survival and which may play important roles in bacterial virulence are often carried on mobile elements, such as plasmids and pathogenicity islands (PAIs). In the present study, we identified and characterized a ferric dicitrate uptake system (Fec) in Shigella flexneri serotype 2a that is encoded by a novel PAI termed the Shigella resistance locus (SRL) PAI. The fec genes are transcribed in S. flexneri, and complementation of a fec deletion in Escherichia coli demonstrated that they are functional. However, insertional inactivation of fecI, leading to a loss in fec gene expression, did not impair the growth of the parent strain of S. flexneri in iron-limited culture media, suggesting that S. flexneri carries additional iron uptake systems capable of compensating for the loss of Fec-mediated iron uptake. DNA sequence analysis showed that the fec genes are linked to a cluster of multiple antibiotic resistance determinants, designated the SRL, on the chromosome of S. flexneri 2a. Both the SRL and fec loci are carried on the 66,257-bp SRL PAI, which has integrated into the serX tRNA gene and which carries at least 22 prophage-related open reading frames, including one for a P4-like integrase. This is the first example of a PAI that carries genes encoding antibiotic resistance and the first report of a ferric dicitrate uptake system in Shigella.Pathogenicity islands (PAIs) are increasingly recognized as playing a vital role in bacterial virulence. PAIs are distinct virulence cassettes that often integrate into tRNA genes and encode bacteriophage-like integrases. Such islands may occupy large regions of the chromosome and often carry mobile elements, such as insertion sequences and transposons (25). PAIs have been found in many bacterial species, including Yersinia spp. (9, 13), enteropathogenic, enterohemorrhagic, and uropathogenic Escherichia coli (24,38,51), Salmonella enterica serovar Typhimurium (61), Vibrio cholerae (32), Helicobacter pylori (14), and Shigella flexneri (2,42,57,71). Some strains of uropathogenic E. coli and S. enterica serovar Typhimurium may harbor at least five PAIs (19,74). A variety of virulence determinants may be carried on PAIs, including genes encoding fimbriae, hemolysins (31, 64), type III secretion systems (15, 27), and iron uptake systems (13,42,71,75). Various Shigella spp. produce the siderophores enterobactin and/or aerobactin, which are involved in iron uptake (34, 50). The aerobactin locus in S. flexneri was recently shown to be carried on the SHI-2 PAI (42, 71). This was the first report of an iron transport system being carried on a PAI in Shigella.A number of PAI-like elements in Shigella spp. have been described. These include the SHI-2 PAI and a family of structurally related elements (42, 71) and the she PAI, which also belongs to a larger family of structurally related elements (2, 57). One of the characteristics of PAIs is their tendency to excise spontaneously from their sites of integration in the chromosome (26). In...

In this study, we determined the boundaries of a 99-kb deletable element of Shigella flexneri 2a strain YSH6000. The element, designated the multiple-antibiotic resistance deletable element (MRDE), had recently been found to contain a 66-kb pathogenicity island (PAI)-like element (designated the SRL PAI) which carries the Shigella resistance locus (SRL), encoding resistance determinants to streptomycin, ampicillin, chloramphenicol, and tetracycline. The YSH6000 MRDE was found to be flanked by two identical IS91 elements present at the S. flexneri homologs of the Escherichia coli genes putA and mdoA on NotI fragment D. Sequence data from two YSH6000-derived MRDE deletants, YSH6000T and S2430, revealed that deletion of the MRDE occurred between the two flanking IS91 elements, resulting in a single IS91 element spanning the two original IS91 loci. Selection for the loss of tetracycline resistance confirmed that the MRDE deletion occurred reproducibly from the same chromosomal site and also showed that the SRL PAI and the SRL itself were capable of independent deletion from the chromosome, thus revealing a unique set of nested deletions. The excision frequency of the SRL PAI was estimated to be 10 ؊5 per cell in the wild type, and mutation of a P4-like integrase gene (int) at the left end of the SRL PAI revealed that int mediates precise deletion of the PAI.

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SummaryThe she pathogenicity island (PAI) is a chromosomal, laterally acquired, integrative element of Shigella flexneri that carries genes with established or putative roles in virulence. We demonstrate that spontaneous, precise excision of the element from its integration site in the 3 ¢ ¢ ¢ ¢ terminus of the pheV tRNA gene is mediated by an integrase gene ( int ) and a gene designated rox (regulator of excision), both of which are carried on the she PAI. Integrase-mediated excision occurs via recombination between a 22 bp sequence at the 3 ¢ ¢ ¢ ¢ terminus of pheV and an imperfect direct repeat at the pheV -distal boundary of the PAI. Excision leads to the formation of a circular episomal form of the PAI, reminiscent of circular excision intermediates of other mobile elements that are substrates for lateral transfer processes such as conjugation, packaging into phage particles and recombinase-mediated integration into the chromosome. The circle junction consists of the pheV -proximal and pheV -distal boundaries of the PAI converging on a sequence identical to 22 bp at the 3 ¢ ¢ ¢ ¢ terminus of pheV . The isolated circle was transferred to Escherichia coli where it integrated specifically into phe tRNA genes, as it does in S. flexneri , independently of recA . We also demonstrate that Rox stimulates, but is not essential for, excision of the she PAI in an integrase-dependent manner. However, Rox does not stimulate excision by activating the transcription of the she PAI integrase gene, suggesting that it has an excisionase function similar to that of a related protein from the P4 satellite element of phage P2.