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 β-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.

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum

“…Indeed, horizontally acquired genes that have a useful function are maintained as it follows a strategy of colonization and adaptation to the environment. Our findings confirm previous results showing that HT particularly affects the genes involved in lipid metabolism, signal transduction and membrane transport in PVC bacteria, and genes specific to outer membrane (such as O-antigen polymerase and outer membrane efflux protein) in some Planctomycetes [ 43 , 86 , 87 ]. Since, the intracytoplasmic membrane of compartmentalized bacteria is a lipid bilayer, we can assume that the over-representation of the two functions in the genes transferred could be related to the cell plan of the bacteria.…”

Global and Targeted Lipid Analysis of Gemmata obscuriglobus Reveals the Presence of Lipopolysaccharide, a Signature of the Classical Gram-Negative Outer Membrane

“…The proteinaceous exterior of G. obscuriglobus has not been shown to constitute a surface layer (S-layer), typically composed of only one or two proteins in a lattice configuration, like that found in some other bacteria, including archaea and the planctomycete "Candidatus Kuenenia stuttgartiensis" (13,22,23). The original cell wall analysis of G. obscuriglobus by Stackebrandt et al (18) found the cell wall composition to include many amino acids, and the ability of the G. obscuriglobus cell to maintain its integrity was demonstrated by the finding that cell sacculi retained their native cell morphology after 10% SDS treatment (18), thus exhibiting resistance to SDS that is more like that of cells that have a peptidoglycan-containing murein sacculus (21). Despite that resistance ability, the cell wall of G. obscuriglobus was actually found in that study not to contain muramic acid and diaminopimelic acid, which are considered peptidoglycan markers (18).…”

“…The absence of peptidoglycan and presence of a proteinaceous cell wall (18) had long been distinguishing planctomycete features that led to the proposal of a unique cell plan for all planctomycetes (3,5,6,13,19). The proteinaceous barrier was previously suggested to substitute for other classical Gram-negative cell features, such as cell surface protection more typically provided by O antigen (20), a rigid structural framework in place of peptidoglycan (13), and possibly as an attachment platform for degradative enzymes, as in a related species, Rhodopirellula baltica (21). The proteinaceous exterior of G. obscuriglobus has not been shown to constitute a surface layer (S-layer), typically composed of only one or two proteins in a lattice configuration, like that found in some other bacteria, including archaea and the planctomycete "Candidatus Kuenenia stuttgartiensis" (13,22,23).…”

Evolution of microbial dynamics with the introduction of real seawater portions in a low-strength feeding anammox process

“…The pie charts represent the relative abundances of relevant OTU sequences. The trees based on Jukes-Cantor distance was constructed using Mega 7.0 with a bootstrap value of 1000 would drive the enzyme-encoding sodium pumping NADH: quinone oxidoreductase (sodium-NQR) and Na + -ATPases to transport sodium ion into cell for smf generation, rather than proton motive force (Paparoditis et al 2014). Next, the enzyme-encoding Na + -translocating (RNF) is activated by the smf and pump Na + out with reduction of ferredoxin for carbon metabolism (de Almeida et al 2016).…”