Paparoditis Philipp, Västermark Ake, Le Andrew J, Fuerst John A, Saier Milton H
Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093-0116, USA.
Biochim Biophys Acta. 2014 Jan;1838(1 Pt B):193-215. doi: 10.1016/j.bbamem.2013.08.007. Epub 2013 Aug 19.
Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.
波罗的海玫瑰单胞菌（R. baltica）是一种浮霉菌，已知其具有细胞内膜。由于其独特的细胞结构和生态意义，我们对其跨膜转运蛋白进行了全面分析。针对转运蛋白分类数据库（TCDB）对波罗的海玫瑰单胞菌的完整蛋白质组进行筛选，以识别可识别的整合膜转运蛋白。共高度可靠地鉴定出342种蛋白质，这些蛋白质可分为几个不同类别。除了数量较少的其他类别外，波罗的海玫瑰单胞菌在其基因组中编码通道蛋白（12%）、次级载体（33%）和初级主动转运蛋白（41%）。相对于大多数非海洋细菌，波罗的海玫瑰单胞菌拥有更多的钠依赖性同向转运体，但质子依赖性同向转运体较少，并且它具有二甲基亚砜（DMSO）和三甲胺氧化物（TMAO）还原酶，这与其富含Na⁺的海洋环境一致。波罗的海玫瑰单胞菌还拥有一种Na⁺转运型NADH：醌脱氢酶（Na⁺-NDH）、一种Na⁺外流脱羧酶、两个Na⁺输出ABC泵、两个Na⁺转运型F型ATP酶、两个Na⁺：H⁺反向转运体和两个K⁺：H⁺反向转运体。鞭毛运动可能依赖于钠电化学梯度。令人惊讶的是，波罗的海玫瑰单胞菌还拥有一整套与α-变形菌和真核线粒体中存在的类似的H⁺转运电子传递复合物。所鉴定的转运蛋白被证明是细菌域的典型特征，几乎没有或没有迹象表明存在真核型转运蛋白。然而，鉴定出了功能未知的新型多跨膜蛋白，其中一些仅在玫瑰单胞菌属物种中发现，但其他一些则广泛分布于细菌中。这些分析得出了关于波罗的海玫瑰单胞菌的生理学、生态学和进化的预测。
