Diverse Ecological Strategies Are Encoded by Streptococcus pneumoniae Bacteriocin-Like Peptides.
Diverse Ecological Strategies Are Encoded by Streptococcus pneumoniae Bacteriocin-Like Peptides.
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DOI：
10.1093/gbe/evw055
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发表时间：
2016-04-13
影响因子：
3.3
通讯作者：
Rozen DE
中科院分区：
文献类型：
--
作者：
Miller EL;Abrudan MI;Roberts IS;Rozen DE
条件致病菌肺炎链球菌通常在人鼻咽部无症状地携带。由于与其他肺炎球菌菌株的共定植率很高，种内竞争相互作用部分决定了菌株的携带持续时间，从而决定了它们致病的潜力。这些相互作用可以由细菌素介导，例如由blp（细菌素样肽）基因座编码的IIb型细菌素。为了了解blp的多样性和进化，我们对4,418个肺炎球菌基因组进行了生物信息学分析，其中包括168个新测序的基因组。我们描述了基因组组织各个层次的巨大变化：基因存在/不存在，基因顺序和等位基因多样性。如果我们做出极端和天真的假设，假设这个操纵子中的所有基因都可以随机分类，这种变异可能导致1015种不同的细菌素相关表型，每种表型都可能代表一种独特的生态策略;然而，我们提供了几种解释，为什么这种极端没有实现。虽然稀疏分析表明，独特的策略的数量是不饱和的，即使在采样数千个基因组，我们表明，变化既不是无界的，也不是随机的。我们划定三个细菌素组，其中包含组特异性细菌素，免疫基因，和blp操纵子基因顺序，并认为，这种组织的地方实现生态策略的约束。我们还表明，生态策略的多样性显着限制肺炎球菌的克隆和克隆结构。通过研究blp操纵子内等位基因之间的关联模式，我们发现，细菌素基因，这被认为是成对的功能，可以发现与广泛的多样性的合作伙伴等位基因和免疫基因，这种整体缺乏等位基因的保真度可能有助于该操纵子的流体结构。我们的研究结果阐明了全球肺炎球菌种群中拮抗生态策略的多样性，并强调了blp细菌素在鼻咽内竞争中的潜在作用。
The opportunistic pathogen Streptococcus pneumoniae is commonly carried asymptomatically in the human nasopharynx. Due to high rates of cocolonization with other pneumococcus strains, intraspecific competitive interactions partly determine the carriage duration of strains and thereby their potential to cause disease. These interactions may be mediated by bacteriocins, such as the type IIb bacteriocins encoded by the blp (bacteriocin-like peptide) locus. To understand blp diversity and evolution, we undertook a bioinformatic analysis of 4,418 pneumococcal genomes, including 168 newly sequenced genomes. We describe immense variation at all levels of genomic organization: Gene presence/absence, gene order, and allelic diversity. If we make the extreme and naive hypothesis that assumes all genes in this operon can assort randomly, this variation could lead to 1015 distinct bacteriocin-related phenotypes, each potentially representing a unique ecological strategy; however, we provide several explanations for why this extreme is not realized. Although rarefaction analysis indicates that the number of unique strategies is not saturated, even after sampling thousands of genomes, we show that the variation is neither unbounded nor random. We delimit three bacteriocin groups, which contain group-specific bacteriocins, immunity genes, and blp operon gene order, and argue that this organization places a constraint on realized ecological strategies. We additionally show that ecological strategy diversity is significantly constrained by pneumococcal phylogeny and clonal structure. By examining patterns of association between alleles within the blp operon, we show that bacteriocin genes, which were believed to function in pairs, can be found with a broad diversity of partner alleles and immunity genes; this overall lack of allelic fidelity likely contributes to the fluid structure of this operon. Our results clarify the diversity of antagonistic ecological strategies in the global pneumococcal population and highlight the potential role of blp bacteriocins in competition within the nasopharynx.