Deciphering Gram-negative phage-inducible chromosomal island strategies for spreading in nature

单一物种内的细菌基因组在基因含量上差异很大，这一概念并不新鲜。然而，直到基因组时代的到来，这种现象才得到了正确的理解。不仅基因组大小不同；在来自特定物种的不同菌株中存在的大量基因甚至不相关，即在其他菌株中没有同源基因。这些基因大多携带在移动遗传元件（MGEs）上，包括质粒、噬菌体、致病性岛、转座子或整合子，它们可以在细菌之间潜在地转移。因此，现在假设水平基因转移（HGT）在细菌进化中起着极其重要的作用。事实上，据估计，任何一种细菌的现存遗传成分中，约有20%是从其他生物体中获得的。其中可能有一半是由MGEs组成的，它们在物种内部和物种之间自由移动，偶尔也会跨越属间边界。在兼性病原体中，MGEs主要负责抗生素耐药性、环境适应和宿主组织对生命的各种适应，我们认为这是发病机制。在大多数致病菌中，所有已知种类的细菌MGEs都可能参与致病机制，特别引人注目的是，基本上所有引起特定毒素介导疾病的细菌毒素-毒素-如PVL肺炎，白喉，痢疾，中毒性休克综合征，食物中毒，坏死性肺炎，烫伤皮肤综合征，肉毒杆菌中毒，溶血性尿毒症综合征或坏死性筋膜炎，都是由MGEs编码的。这个应用程序代表了一个长期和高生产力的研究计划的高潮，从2003年开始，一直延伸到现在。在此期间，我们描述了一个新的移动葡萄球菌致病性岛家族，SaPIs，它是几种重要超级抗原的唯一来源，包括中毒性休克综合征毒素-1和肠毒素B和C，以及与宿主适应相关的其他毒力因子的来源。毫不奇怪，这些元素不仅局限于葡萄球菌，而且广泛存在于革兰氏阳性细菌中。最近，我们也证明了类似的元素在革兰氏阴性菌中广泛存在，符合一类独特的MGEs，噬菌体诱导的染色体岛（PICIs）。我们认为pici在细菌世界中广泛传播，并且比宿主生物分化得慢得多。如果这是真的，这些发现代表了一类新的MGE的发现，它对细菌世界的横向基因转移和毒力有广泛的影响。虽然我们之前的研究已经破解了存在于革兰氏阳性细菌中的PICI元素是如何被诱导和水平转移的，但在革兰氏阴性PICI的生物学中，仍有两个主要问题有待确定：1)这些元素如何感知它们的辅助噬菌体的存在，以及2)它们如何劫持噬菌体机制以进行自己的特定包装，阻止噬菌体繁殖。破译这两个过程对于理解这些元素如何在自然界中传播至关重要。在这个项目中，我们将回答这些问题。通过实现这些目标，我们将建立涉及细菌进化和毒力的致病性岛的新范式，并将提供阻止致病性岛传播和新型细菌毒力克隆出现的策略。

The concept that bacterial genomes within a single species can vary widely in gene content is not new. However, it was only with the arrival of the genomic era that the phenomenon has been properly understood. Not only was the genome size different; a significant number of the genes present in different strains from a specific species were not even related i.e. had no homologous genes in the others. Most of these genes were carried on mobile genetics elements (MGEs), including plasmids, bacteriophages, pathogenicity islands, transposons or integrons, which can be potentially transferred among bacteria. Thus, it is now assumed that horizontal gene transfer (HGT) has had an extremely important role in bacterial evolution. Indeed it has been estimated that some 20% of the extant genetic content of any given bacterial species has been acquired from other organisms. Perhaps half of this consists of MGEs, which have moved freely within and between species, and have occasionally crossed intergeneric boundaries. In facultative pathogens, MGEs are largely responsible for antibiotic resistance, environmental adaptations and the wide variety of adaptations to life in host tissues that we perceive as pathogenesis. In most pathogenic bacteria, all known classes of bacterial MGEs may contribute to pathogenesis, and it is particularly striking that essentially all of the bacterial toxins that cause specific toxin-mediated diseases - toxinoses - such as PVL pneumonia, diphtheria, dysentery, toxic shock syndrome, food poisoning, necrotizing pneumonia, scalded skin syndrome, botulism, hemolytic-uremic syndrome or necrotizing fasciitis, are encoded by MGEs.This application represents the culmination of a long and highly productive research program starting in 2003 and extending to the present. During this time we have characterised a novel family of mobile staphylococcal pathogenicity islands, the SaPIs, which are the only source of several important superantigens, including toxic shock syndrome toxin-1 and enterotoxins B and C, as well as the source for other virulence factors related to host adaptation. Not surprisingly, these elements are not just confined to the Staphylococci, but are widespread within Gram-positive bacteria. Recently, we have also demonstrated that similar elements occur widely in Gram-negative bacteria, conforming a unique class of MGEs, the phage-inducible chromosomal islands (PICIs). We suggest that the PICIs have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms. If true, these findings represent the discovery of a new class of MGE, which have a broad impact on lateral gene transfer and virulence in the bacterial world.Although our previous studies have deciphered how the PICI elements present in the Gram-positive bacteria are induced and horizontally transferred, two main questions remain to be determined in the biology of the Gram-negative PICIs: i) how these elements sense the presence of their helper phages, and ii) how they hijack the phage machinery for their own specific packaging, blocking phage reproduction. To decipher these two processes is of vital importance to understand how these elements spread in nature. In this project we will answer these questions. By achieving these objectives we will establish new paradigms involving pathogenicity islands in bacterial evolution and virulence, and will provide strategies to block pathogenicity island dissemination and the emergence of novel bacterial virulent clones.