Ramisetty Bhaskar Chandra Mohan, Sudhakari Pavithra Anantharaman
Laboratory of Molecular Biology and Evolution, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
Front Genet. 2019 Feb 12;10:65. doi: 10.3389/fgene.2019.00065. eCollection 2019.
Bacterial genomes are highly plastic allowing the generation of variants through mutations and acquisition of genetic information. The fittest variants are then selected by the econiche thereby allowing the bacterial adaptation and colonization of the habitat. Larger genomes, however, may impose metabolic burden and hence bacterial genomes are optimized by the loss of frivolous genetic information. The activity of temperate bacteriophages has acute consequences on the bacterial population as well as the bacterial genome through lytic and lysogenic cycles. Lysogeny is a selective advantage as the prophage provides immunity to the lysogen against secondary phage attack. Since the non-lysogens are eliminated by the lytic phages, lysogens multiply and colonize the habitat. Nevertheless, all lysogens have an imminent risk of lytic cycle activation and cell lysis. However, a mutation in the attachment sites or in the genes that encode the specific recombinase responsible for prophage excision could result in 'grounding' of the prophage. Since the lysogens with grounded prophage are immune to respective phage infection as well as dodge the induction of lytic cycle, we hypothesize that the selection of these mutant lysogens is favored relative to their normal lysogenic counterparts. These grounded prophages offer several advantages to the bacterial genome evolution through propensity for genetic variations including inversions, deletions, and insertions via horizontal gene transfer. We propose that the grounded prophages expedite bacterial genome evolution by acting as 'genetic buffer zones' thereby increasing the frequency as well as the diversity of variations on which natural selection favors the beneficial variants. The grounded prophages are also hotspots for horizontal gene transfer wherein several ecologically significant genes such as those involved in stress tolerance, antimicrobial resistance, and novel metabolic pathways, are integrated. Moreover, the high frequency of genetic changes within prophages also allows proportionate probability for the genesis of genetic information. Through sequence analyses of well-characterized prophages we exemplify various roles of grounded prophages in ecology and evolution. Therefore, the temperate prophages are one of the most significant drivers of bacterial genome evolution and sites of biogenesis of genetic information.
细菌基因组具有高度可塑性，可通过突变和获取遗传信息产生变异。然后，最适应环境的变异体被生态位选择，从而使细菌能够适应并定殖于栖息地。然而，较大的基因组可能会带来代谢负担，因此细菌基因组会通过丢失无用的遗传信息而得到优化。温和噬菌体的活动通过裂解周期和溶原周期对细菌群体以及细菌基因组产生严重影响。溶原性是一种选择优势，因为原噬菌体为溶原菌提供了针对二次噬菌体攻击的免疫力。由于非溶原菌会被裂解性噬菌体消灭，溶原菌得以繁殖并定殖于栖息地。然而，所有溶原菌都面临着裂解周期激活和细胞裂解的紧迫风险。然而，附着位点或编码负责原噬菌体切除的特定重组酶的基因发生突变，可能导致原噬菌体“固定”。由于带有固定原噬菌体的溶原菌对相应噬菌体感染具有免疫力，并且能够避免裂解周期的诱导，我们推测相对于正常的溶原对应物，这些突变溶原菌的选择更受青睐。这些固定的原噬菌体通过促进包括倒位、缺失和通过水平基因转移进行插入等遗传变异，为细菌基因组进化提供了几个优势。我们提出，固定的原噬菌体通过充当“遗传缓冲区”来加速细菌基因组进化，从而增加变异的频率和多样性，自然选择会青睐这些有益变异。固定的原噬菌体也是水平基因转移的热点，其中整合了几个具有生态意义的基因，如参与应激耐受、抗菌抗性和新代谢途径的基因。此外，原噬菌体内遗传变化的高频率也为遗传信息的产生提供了相应的可能性。通过对特征明确的原噬菌体进行序列分析，我们举例说明了固定原噬菌体在生态和进化中的各种作用。因此，温和噬菌体是细菌基因组进化的最重要驱动因素之一，也是遗传信息生物发生的场所。
