Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes

Abstract

Whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. For each organism, the complete set of membrane transport systems was identified with predicted functions, and classified into protein families based on the transporter classification system. Organisms with larger genome sizes generally possessed a relatively greater number of transport systems. In prokaryotes and unicellular eukaryotes, the significant factor in the increase in transporter content with genome size was a greater diversity of transporter types. In contrast, in multicellular eukaryotes, greater number of paralogs in specific transporter families was the more important factor in the increase in transporter content with genome size. Both eukaryotic and prokaryotic intracellular pathogens and endosymbionts exhibited markedly limited transport capabilities. Hierarchical clustering of phylogenetic profiles of transporter families, derived from the presence or absence of a certain transporter family, showed that clustering patterns of organisms were correlated to both their evolutionary history and their overall physiology and lifestyles.

Figure 1. Venn Diagram Showing the Distribution of Transporter Families across the Three Domains of Life

Figure 2. Numbers of Recognized Transport Proteins and Percentage of Total ORFs

The overall numbers of recognized transport proteins (A) and percentage of total ORFs encoding transport proteins (B) were compared for the 141 organisms analyzed. Species from distinct phylogenetic groups are labeled with different colors. The prokaryotic and eukaryotic obligate intracellular parasites/pathogens are marked with red stars.

Figure 3. Number of Total ORFs versus Number of Distinct Transporter Families or Average Number of Paralogs per Family

The number of total ORFs in the genome for each of the 141 sequenced prokaryotic and eukaryotic organisms (x-axis) was plotted as a function of either the number of distinct transporter families (A) or the average number of paralogs per family (B) (y-axis). Blue diamonds represent prokaryotic organisms and red squares represent eukaryotic organisms. Trend line and power correlation R ² value are shown for prokaryotes and eukaryotes, respectively. A group of α-Proteobacteria are enclosed by a circle (see text for discussion).

Figure 4. Phylogenetic Profiling of Transporter Families

Phylogenetic profiles were created for each transporter family. Each profile is a string with 141 entries (number of organisms analyzed). If a given family is present in an organism, the value one is assigned at this position (red). If not, zero is assigned (black). Organisms and transporter families were clustered according to the similarity of their phylogenetic profiles.

Figure 5. Hierarchial Clustering of Phylogenetic Profiles of Obligate Intracellular Pathogens/Symbionts versus Soil/Plant-Associated Microbes

Detailed view of two clusters of organisms generated by hierarchical clustering of their phylogenetic profiles of transporter families: obligate intracellular pathogens/symbionts and soil/plant-associated microbes.

Figure 6. Venn Diagrams Showing the Distribution of Transporter Families among Species Belonging to the Same Genus

(A) Transporter family distribution among three Pseudomonas species. (B) Transporter family distribution among three Corynebacterium species.