Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica

Abstract

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.

Keywords: Cellular energization; Electron transport; Marine ecology; Planctomycetes; Sodium motive force; Transport proteins.

Figure 1

Distribution of transporters based on TC (A) classes and (B) subclasses in R. baltica.

Figure 1

Distribution of transporters based on TC (A) classes and (B) subclasses in R. baltica.

Figure 2

Transporter distribution based on (A) substrate groups and (B) subgroups in R. baltica.

Figure 2

Transporter distribution based on (A) substrate groups and (B) subgroups in R. baltica.

Figure 3

Topological analysis of (A) all R. baltica integral membrane transport proteins included in this study, (B) channels, (C) secondary carriers and (D) primary active transporters. Proteins predicted to have 0 TMSs in either the query or the hit sequence were eliminated from this study as described under Methods (section 2.2).

Figure 3

Topological analysis of (A) all R. baltica integral membrane transport proteins included in this study, (B) channels, (C) secondary carriers and (D) primary active transporters. Proteins predicted to have 0 TMSs in either the query or the hit sequence were eliminated from this study as described under Methods (section 2.2).

Figure 3

Topological analysis of (A) all R. baltica integral membrane transport proteins included in this study, (B) channels, (C) secondary carriers and (D) primary active transporters. Proteins predicted to have 0 TMSs in either the query or the hit sequence were eliminated from this study as described under Methods (section 2.2).

Figure 3

Topological analysis of (A) all R. baltica integral membrane transport proteins included in this study, (B) channels, (C) secondary carriers and (D) primary active transporters. Proteins predicted to have 0 TMSs in either the query or the hit sequence were eliminated from this study as described under Methods (section 2.2).

Figure 4

Schematic interpretation of the unusual dual occurrence of several Na⁺-transport systems in the compartmentalized R. baltica cell. The cell wall (CW) is color coded brown. F-type ATPases are proposed to be present in both the intracellular membrane (ICM; color coded green) and the cytoplasmic membrane (CM; dark blue) as has been documented for the two membranes in Candidatus Kuenenia stuttgartiensis [145]. This would imply that there is a proton motive force (pmf) and/or a sodium-motive force (smf) across both membranes which might also suggest that both membranes contain constituents of electron transfer chains although this has not been demonstrated for R. baltica. The yellow compartment is the paryphoplasm and the light blue compartment is the pirellulosome. The nucleoid is represented by a tangled red line. This color-coding is adopted from Fuerst and Sagulenko (2013) [23]. ‘Parypho’ is derived from the classical Greek word paryphe for border of a robe. The nucleoid of the R. baltica cell is only enclosed by a single membrane, that of the ICM, not to be confused with the structure of Gemmata obscuriglobus, which has a nuclear envelope within the pirellulosome surrounding the nucleoid. The whole compartment enclosed by the ICM is called the pirellulosome, but there is no additional nuclear body as in Gemmata, so the nucleoid is naked and bounded only by the ICM as are the other pirellulosome contents. No periplasm between the CW and CM is drawn because no evidence for its existence has been published. This arrangement could result in the generation of an smf as well as a pmf across both the CM and the ICM, and the former could be used for ATP synthesis via the two distinct F-type-ATPases, F-ATPase-1 and F-ATPase-2 in the CM and ICM. The diagram illustrates the use of dual Na⁺:H⁺ antiporters, Nha-1 and Nha-2 as well as two ABC-type Na⁺ pumps, ABC-1 and ABC-2.