Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany.
Department of Physical Chemistry and Microreaction Technology, Institute for Chemistry and Biotechnique, Technische Universität Ilmenau, Ilmenau, Germany.
mSphere. 2024 Oct 29;9(10):e0068524. doi: 10.1128/msphere.00685-24. Epub 2024 Sep 18.
KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter is utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. KT2440 is the best-studied non-methylotroph in the context of Ln-utilization. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln on transcriptome-wide gene expression when growing KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, and Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, and Yb) had a positive effect on growth, whereas supplementation with heavy Ln (Dy, Ho, Er, and Yb) exerted fitness costs. These were likely a consequence of mismetallation and non-utilizable Ln interfering with Ln sensing and signaling. The measured amounts of cell-associated Ln varied between elements. Gene expression analysis suggested that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We expanded our understanding of the lanthanide (Ln) switch in KT2440, demonstrating that it adjusts the levels of and transcripts based on the availability of Ln. We propose that the usability of Ln influences the bacterium's response to different Ln elements.IMPORTANCEThe Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH in response to Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a fine-tuning mechanism of Ca- and Ln-dependent PQQ ADH in KT2440 on the transcriptome level. The response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.
KT2440 是一种普遍存在于土壤中的细菌,能够代谢顽固和挥发性的碳源。后者由两种冗余的、依赖钙和镧系元素(Ln)的吡咯喹啉醌依赖性醇脱氢酶(PQQ ADH),即 PedE 和 PedH 利用,它们的表达受 Ln 可用性的调节。KT2440 是在 Ln 利用方面研究最多的非甲基营养菌。结合微流控培养和单细胞元素分析,当用 2-苯乙醇作为碳和能源生长时,我们研究了轻 Ln(La、Ce 和 Nd)和重 Ln(Dy、Ho、Er 和 Yb)混合物对整个转录组基因表达的影响。轻 Ln(La、Ce 和 Nd)和轻 Ln 与重 Ln 的混合物(La、Ce、Nd、Dy、Ho、Er 和 Yb)对生长有积极影响,而重 Ln(Dy、Ho、Er 和 Yb)的补充则会产生适应性成本。这可能是由于错配位和不可利用的 Ln 干扰了 Ln 感应和信号传递所致。测量的细胞相关 Ln 量因元素而异。基因表达分析表明,Ln 感应和信号机制,即双组分系统 PedS2R2 和 PedH,对(不可用)Ln 的反应不同。我们扩展了对 KT2440 中镧系元素(Ln)开关的理解,证明它根据 Ln 的可用性调整 和 转录本的水平。我们提出,Ln 的可用性影响细菌对不同 Ln 元素的反应。
重要性
Ln 开关,即生物体中同时存在 Ca 和 Ln 依赖性 PQQ ADH 对 Ln 可用性的反向调节,是我们理解 Ln 利用的核心。尽管细菌对轻 Ln 的偏好是众所周知的,但不同 Ln(轻和重)对生长和基因表达的影响很少被研究。我们在转录组水平上为 KT2440 中 Ca 和 Ln 依赖性 PQQ ADH 的精细调节机制提供了证据。对(不可用)Ln 的反应因元素而异。Ln 通常在自然界中共同存在。我们的研究结果强调了 Ln 利用微生物必须能够区分 Ln 才能有效地利用它们。考虑到许多微生物类群中存在 Ln 依赖性蛋白,需要开展更多关于 Ln 感应和信号传递的工作。Ln 的可用性可能需要针对 Ln 利用进行不同的适应。