Harnessing natural diversity to probe metabolic pathways.
Harnessing natural diversity to probe metabolic pathways.
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DOI：
10.1371/journal.pgen.0010080
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发表时间：
2005-12
期刊：
影响因子：
4.5
通讯作者：
Lindquist, SL
中科院分区：
文献类型：
--
作者：
Homann, OR;Cai, HJ;Becker, JM;Lindquist, SL
对酿酒酵母细胞过程的分析主要依赖于少量高度驯化的实验室菌株，留下了模式生物广泛的自然遗传多样性，很大程度上是未被开发和利用的。我们询问这种多样性是否可以用来丰富我们对基本生物过程的理解。作为一个测试案例，我们考察了一个简单的特性：利用二/三肽作为氮源。进口小肽的能力可能处于相反的选择压力下(营养利用与毒素脆弱性)，因此可能由不同的途径和策略塑造。到目前为止，酿酒酵母对二肽的利用仅归因于单一蛋白质Ptr2p转运蛋白的活性。使用高通量表型和几个不同的遗传菌株，我们确定了以前未知的细胞活动，导致了这一特征。我们发现，Dal5p尿囊酸/尿苷琥珀酸渗透酶也能够促进二/三肽的转运。此外，即使在没有Dal5p和Ptr2p的情况下，一个额外的活性--几乎可以肯定是质周天冬酰胺酶II Asp3p--通过不同的策略促进带有C-末端天冬酰胺残基的二肽的利用。另一种尚不确定的活性使带有C-末端精氨酸残基的二肽得以利用。这些活性对二/三肽利用的相对贡献在所分析的菌株中有所不同，这些菌株对有毒二肽的脆弱性也不同。只有通过对多个菌株的遗传多样性进行采样，我们才能在这一代谢途径中发现几个以前未被认识到的复杂性层。高通量表型有助于快速探索生物复杂性的分子基础，允许未来对驱动微生物进化的选择压力进行详细研究。模型生物使研究人员能够以精致的细节描述基本的生物过程。Homann等人。认为这一知识库提供了一个独特的机会，可以利用在同一物种的不同分离株中发现的自然遗传变异来获得新的见解。使用高通量技术来测定生长，Homann等人。发现酿酒酵母的实验室菌株、葡萄园菌株和临床菌株利用二/三肽作为营养源的能力有很大的不同。这导致了新的二/三肽利用活性的发现和它们的特异性的阐述。这些活性强度的变化决定了在给定菌株中优先利用的二/三肽的谱。反过来，这又影响了这些菌株对一种有毒多肽的脆弱性，这种有毒多肽利用运输机制进入细胞。这提出了一种有趣的可能性，即相反的选择压力，即利用二/三肽作为营养源的好处被进口有毒多肽的风险所抵消，可能塑造了观察到的自然多样性。模式生物分离株之间存在的自然遗传多样性预示着一个丰富的资源，可以用来揭示分子途径的复杂性，并探索塑造它们的选择压力。
Analyses of cellular processes in the yeast Saccharomyces cerevisiae rely primarily upon a small number of highly domesticated laboratory strains, leaving the extensive natural genetic diversity of the model organism largely unexplored and unexploited. We asked if this diversity could be used to enrich our understanding of basic biological processes. As a test case, we examined a simple trait: the utilization of di/tripeptides as nitrogen sources. The capacity to import small peptides is likely to be under opposing selective pressures (nutrient utilization versus toxin vulnerability) and may therefore be sculpted by diverse pathways and strategies. Hitherto, dipeptide utilization in S. cerevisiae was solely ascribed to the activity of a single protein, the Ptr2p transporter. Using high-throughput phenotyping and several genetically diverse strains, we identified previously unknown cellular activities that contribute to this trait. We find that the Dal5p allantoate/ureidosuccinate permease is also capable of facilitating di/tripeptide transport. Moreover, even in the absence of Dal5p and Ptr2p, an additional activity—almost certainly the periplasmic asparaginase II Asp3p—facilitates the utilization of dipeptides with C-terminal asparagine residues by a different strategy. Another, as-yet-unidentified activity enables the utilization of dipeptides with C-terminal arginine residues. The relative contributions of these activities to the utilization of di/tripeptides vary among the strains analyzed, as does the vulnerability of these strains to a toxic dipeptide. Only by sampling the genetic diversity of multiple strains were we able to uncover several previously unrecognized layers of complexity in this metabolic pathway. High-throughput phenotyping facilitates the rapid exploration of the molecular basis of biological complexity, allowing for future detailed investigation of the selective pressures that drive microbial evolution. Model organisms have allowed researchers to characterize basic biological processes in exquisite detail. Homann et al. suggest that this knowledge base presents a unique opportunity to exploit the natural genetic variation found in diverse isolates of the same species to gain new insights. Using high-throughput technology to assay growth, Homann et al. found that laboratory strains, vineyard isolates, and clinical isolates of the yeast Saccharomyces cerevisiae exhibit very different capacities to utilize di/tripeptides as nutrient sources. This led to the discovery of new di/tripeptide utilization activities and an elaboration of their specificities. Variations in the strength of these activities determine the spectrum of di/tripeptides that are preferentially utilized in a given strain. In turn, this influenced the vulnerability of these strains to a toxic peptide, which exploits the transport machinery to gain entry into the cell. This raises the intriguing possibility that opposing selective pressures, in which the benefit of utilizing di/tripeptides as a nutrient source is offset by the risk of importing toxic peptides, may have shaped the observed natural diversity. The natural genetic diversity present among isolates of model organisms augurs a rich resource for revealing complexities in molecular pathways and exploring the selective pressures that shaped them.
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影响因子：
12.3
作者：
Fay JC;McCullough HL;Sniegowski PD;Eisen MB
通讯作者：
Eisen MB
影响因子：
64.8
作者：
Gavin, AC;Bösche, M;Superti-Furga, G
通讯作者：
Superti-Furga, G
DOI：
10.1016/0005-2736(77)90362-5
发表时间：
1977-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
GRETH, ML;CHEVALLIER, MR;LACROUTE, F
通讯作者：
LACROUTE, F
影响因子：
11.4
作者：
Byrd, C;Turner, GC;Varshavsky, A
通讯作者：
Varshavsky, A
影响因子：
3.2
作者：
CHISHOLM, VT;LEA, HZ;COOPER, TG
通讯作者：
COOPER, TG