Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS

Cooperation and Competition Were Primary Driving Forces for Biological Evolution

BACKGROUND

For many years, scientists have accepted Darwin's conclusion that "Survival of the Fittest" involves successful competition with other organisms for life-endowing molecules and conditions.

SUMMARY

Newly discovered "partial" organisms with minimal genomes that require symbiotic or parasitic relationships for growth and reproduction suggest that cooperation in addition to competition was and still is a primary driving force for survival. These two phenomena are not mutually exclusive, and both can confer a competitive advantage for survival. In fact, cooperation may have been more important in the early evolution of life on earth before autonomous organisms developed, becoming large genome organisms.

KEY MESSAGES

This suggestion has tremendous consequences with respect to our conception of the early evolution of life on earth as well as the appearance of intercellular interactions, multicellularity and the nature of interactions between humans and their societies (e.g., social Darwinism).

The Transporter Classification Database (TCDB): 2021 update

The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified in 15 528 non-redundant transport systems with 1567 tabulated 3D structures, 18 336 reference citations describing 1536 transporter families, of which 26% are members of 82 recognized superfamilies. Overall, this is an increase of over 50% since the last published update of the database in 2016. This comprehensive update of the database contents and features include (i) adoption of a chemical ontology for substrates of transporters, (ii) inclusion of new superfamilies, (iii) a domain-based characterization of transporter families for the identification of new members as well as functional and evolutionary relationships between families, (iv) development of novel software to facilitate curation and use of the database, (v) addition of new subclasses of transport systems including 11 novel types of channels and 3 types of group translocators and (vi) the inclusion of many man-made (artificial) transmembrane pores/channels and carriers.

A Riboflavin Transporter in Bdellovibrio exovorous JSS

The ImpX transporters of the drug/metabolite transporter superfamily were first proposed to transport riboflavin (RF; vitamin B2) based on findings of a cis-regulatory RNA element responding to flavin mononucleotide (an FMN riboswitch). Bdellovibrio exovorous JSS has a homolog belonging to this superfamily. It has 10 TMSs and shows 30% identity to the previously characterized ImpX transporter from Fusobacterium nucleatum. However, the ImpX homolog is not regulated by an FMN-riboswitch. In order to test the putative function of the ImpX homolog from B. exovorous (BexImpX), we cloned and heterologously expressed its gene. We used functional complementation, growth inhibition experiments, direct uptake experiments and inhibition studies, suggesting a high degree of specificity for RF uptake. The EC50 for growth with RF was estimated to be in the range 0.5-1 µM, estimated from the half-maximal RF concentration supporting the growth of a RF auxotrophic Escherichia coli strain, but the Khalf for RF uptake was 20 µM. Transport experiments suggested that the energy source is the proton motive force but that NaCl stimulates uptake. Thus, members of the ImpX family members are capable of RF uptake, not only in RF prototrophic species such as F.  nucleatum, but also in the B2 auxotrophic species, B. exovorous.

Sensitivity of predatory bacteria to different surfactants and their application to check bacterial predation

We evaluated the toxicity of surfactants against different predatory bacteria. Tests with Bdellovibrio bacteriovorus HD100 and SDS, an anionic surfactant, showed the predator was very sensitive; 0.02% SDS completely killed the predatory population (7-log loss; < 10 PFU/ml remaining) both when free-swimming or within the bdelloplast, i.e., intraperiplasmic. Similar results were also observed with B. bacteriovorus 109J and Peredibacter starrii. In contrast, none of the prey (E. coli, Klebsiella pneumoniae, Acinetobacter baumannii, or Pseudomonas sp. DSM 50906) viabilities were negatively affected by SDS. Triton X-100, a nonionic surfactant, was slightly less toxic towards B. bacteriovorus HD100 (viability loss of only 4-log), while two cationic surfactants, i.e., benzalkonium chloride (BZC) and cetyltrimethylammonium bromide (CTAB), were toxic towards both the predator and prey. Based on the above findings, we tested the potential use of SDS as a means to control predation. Addition of 0.02% SDS immediately halted predation based upon the prey bioluminescence, which leveled off and remained steady. This was confirmed using the predator viabilities; no predators were found in any of the samples where SDS was added. Consequently, low concentrations of SDS can be used as a simple means to control B. bacteriovorus HD100 activities.

Comparative genomics of the transportome of Ten Treponema species

Treponema is a diverse bacterial genus, the species of which can be pathogenic, symbiotic, or free living. These treponemes can cause various diseases in humans and other animals, such as periodontal disease, bovine digital dermatitis and animal skin lesions. However, the most important and well-studied disease of treponemes that affects humans is 'syphilis'. This disease is caused by Treponema pallidum subspecie pallidum with 11-12 million new cases around the globe on an annual basis. In this study we analyze the transportome of ten Treponema species, with emphasis on the types of encoded transport proteins and their substrates. Of the ten species examined, two (T. primitia and T. azonutricium) reside as symbionts in the guts of termites; six (T. pallidum, T. paraluiscuniculi, T. pedis, T. denticola, T. putidum and T. brennaborense) are pathogens of either humans or animals, and T. caldarium and T. succinifaciens are avirulent species, the former being thermophilic. All ten species have a repertoire of transport proteins that assists them in residing in their respective ecological niches. For instance, oral pathogens use transport proteins that take up nutrients uniquely present in their ecosystem; they also encode multiple multidrug/macromolecule exporters that protect against antimicrobials and aid in biofilm formation. Proteins of termite gut symbionts convert cellulose into other sugars that can be metabolized by the host. As often observed for pathogens and symbionts, several of these treponemes have reduced genome sizes, and their small genomes correlate with their dependencies on the host. Overall, the transportomes of T. pallidum and other pathogens have a conglomerate of parasitic lifestyle-assisting proteins. For example, a T. pallidum repeat protein (TprK) mediates immune evasion; outer membrane proteins (OMPs) allow nutrient uptake and end product export, and several ABC transporters catalyze sugar uptake, considered pivotal to parasitic lifestyles. Taken together, the results of this study yield new information that may help open new avenues of treponeme research.