Marine Biotechnology Fellowship: Ribosomal RNA Regulation in Marine Bacteria

海洋细菌是海洋生产力和生物地球化学循环中的重要环节。虽然海洋细菌的种类组成在很大程度上是未知的，但有证据表明，大多数海洋细菌是真细菌王国的紫色细菌门的成员。该门包含光合细菌、异养细菌和石养细菌。许多成员能够氧化或还原氮和硫，这在海洋环境中极其重要。这个项目试图确定紫色细菌的RNA/DNA比例和生长速度之间是否存在一般关系。来自海洋紫色细菌完美假单胞菌的新证据表明，RNA/DNA比率和生长速度之间的关系延伸到据信发生在海洋中的低生长速度。此外，P。Perfect tomarina的数据与在接近最大生长速度的肠道细菌上测量的RNA/DNA比率一致。然而，RNA/DNA比率和生长速度之间的这种预测关系是否适用于其他紫色细菌在自然环境中可以存在的整个生长速度范围内，这一预测关系尚未得到广泛建立。为了扩大可用于测量海洋微生物生长速度的rRNA探针库，将采用五步法：1)克隆海洋rRNA基因，并创建海洋rRNA启动子-报告基因融合，以评估是否存在生长速度依赖的调控；2)利用已建立的方法对6个海洋细菌(代表紫色细菌的3个亚类)的RNA-DNA比率与生长速率进行了经验测量；3)研究了海洋细菌中控制rRNA合成的机制；4)筛选海洋细菌基因组中是否存在调节rRNA合成的新基因；5)克隆和测序每个海洋细菌的23个S rRNA亚基，并确定物种特异性区域，这些区域将用于测定南加利福尼亚州海湾海水样品的原位生长速度。如果发现这些紫色细菌的RNA/DNA比例和生长速度之间存在一般关系，调查人员可以例行确定自然样品中大量紫色细菌的存在并测量其生长速度。总之，研究rRNA与生长速度之间的关系，对于rRNA探针在海洋中的未来应用是极其重要的。没有其他大分子可以提供必要的遗传和代谢信息，以评估复杂组合中单一物种微生物的生长速度，而不会有污染的风险。

Marine bacteria are essential links in marine productivity and biogeochemical cycles. Although the species composition of marine bacteria is largely unknown, evidence suggests that most marine bacteria are members of the Purple bacteria phylum of the Eubacterial kingdom. The phylum contains photosynthetic, heterotrophic, and lithotrophic bacteria. Many members are capable of either the oxidation or reduction of nitrogen and sulfur which are extremely important in the marine environment. This project seeks to ascertain if a general relationship between RNA/DNA ratios and growth rate exists for the Purple bacteria. New evidence from the marine Purple bacterium, Pseudomonas perfectomarina, indicates that the relationship between RNA/DNA ratio and growth rate extends to the low growth rates believed to occur in the ocean. Furthermore, the Ps. perfectomarina data is in agreement with the RNA/DNA ratios measured on enteric bacteria at near maximal growth rates. However, it has not been widely established that this predictive relationship between RNA/DNA ratio and growth rate is valid for other Purple bacteria over the complete range of growth rates that can exist in the natural environment. In order to expand the repertoire of rRNA probes that can be used to measure microbial growth rate in the ocean, a five-step approach will be undertaken to: 1) clone the marine rRNA genes and create marine rRNA promoter-reporter gene fusions to assess if there is regulation in a growth rate-dependent manner; 2) empirically measure the RNA-DNA ratio vs growth rate for six marine bacteria (representing three subdivisions of the Purple bacteria) using previously established methods; 3) investigate the mechanisms controlling rRNA synthesis in the marine bacteria; 4) screen the marine bacteria's genomes for the presence of novel genes regulating rRNA synthesis; 5) clone and sequence the 23 S rRNA subunit of each marine bacterium and identify species-specific regions which will be used to assay the in situ growth rate in seawater samples from the Southern California Bight. If a general relationship between RNA/DNA ratios and growth rates are found to exist for these purple bacteria, investigators could routinely determine the presence and measure the growth rates of large numbers of Purple bacteria in natural samples. In conclusion, it is extremely important for the future use of rRNA probes in the ocean that the relationship between rRNA and growth rate be investigated. No other macromolecule can provide the genetic and metabolic information necessary to evaluate the growth rate of a single species of micro-organism in a complex assemblage without the risk of contamination.