Animal(veterinary) Bacterial Secretion Systems (introduction)

Bacterial Secretion Systems

 Introduction 

 Secretion in unicellular species is the transport or translocation of molecules, for example proteins, from the interior of the cell to its exterior. In bacteria secretion is a very important mechanism, either modulating their interactions with their environment for adaptation and survival or establishing interactions with  their eukaryotic hosts for pathogenesis or symbiosis. To overcome the physical barriers of membranes, Gram-negative bacteria use a variety of molecular machines which have been elaborated to secrete a wide range of proteins and other molecules; their functions include biogenesis of organelles (e.g. pili and flagella), virulence, efflux of toxins etc. As  in some cases the secreted proteins are destined to enter host cells (effectors, toxins), some of the secretion systems include extracellular appendices to translocate proteins across the plasma membrane of the host.

With the rapid accumulation of bacterial  genome sequences, our knowledge of the complexity of bacterial protein secretion systems has expanded and several secretion systems have been identified. Gene Ontology has been very useful for describing the components and functions of these systems,  and for capturing the similarities among the diverse systems (Tseng et al., 2009). These analyses along with numerous biochemical studies have revealed the existence of at least six major mechanisms of protein secretion.These pathways are highly conserved throughout the Gram-negative bacterial species and are functionally independent with respect to outer membrane translocation; commonalities exist in the inner membrane transport steps of some systems, with most of them being terminal branches of the general secretion pathway (Sec). The pathways have been numbered Type I, II, III, IV, V and VI. 

In Gram-negative bacteria, some secreted proteins are exported across the inner and outer membranes in a single step via the Type I, III, IV or VI pathways. Other proteins are first exported into the periplasmic space using the universal Sec or two-arginine (Tat) pathways and then translocated across the outer membrane via the Type II, V or less commonly, the Type I or IV machinery. In Gram-positive bacteria, secreted proteins are commonly translocated across the single membrane by the Sec pathway, the two-arginine (Tat) pathway, or the recently identified type VII secretion system. In the following we will briefly survey the six Gram-negative bacterial secretion systems known to modulate interactions with host organisms:

Type I secretion system: 

This system (T1SS) forms a contiguous channel traversing the inner and outer membranes of Gram-negative bacteria. It is a simple system, which consists of only three major components: ATP-binding cassette transporters, Outer Membrane Factors, and Membrane Fusion Proteins. T1SS transports ions and various molecules including proteins of various sizes (20 900 kDa) and non-proteinaceous substrates like cyclic ǃ-glucans and polysaccharides. 

Type II secretion system:

This system (T2SS) is encoded by at least 12 genes and supports the transport of a group of seemingly unrelated proteins across the outer membrane. In  order for these proteins to enter the type II secretion pathway, they have to first translocate across the cytoplasmic membrane via the Sec-system and then fold into a translocation competent conformation in the periplasm. Proteins secreted by T2SS include proteases, cellulases, pectinases, phospholipases, lipases, and toxins which contribute to cell damage and disease. Although Sec-dependent translocation is universal, the T2SS is found only in Gram-negative proteobacteria phylum. A bacterial species may have more than one T2SS.

Type III secretion system: 

These systems (T3SS) are essential mediators of the interaction of many Gram-negative pathogenic proteobacteria (ǂ,  ǃ,  DŽ and  Dž subdivisions) with their human, animal, or plant hosts  and are evolutionarily related to bacterial flagella. The machinery of the T3SS, termed the injectisome, appears to have a common evolutionary origin with the flagellum and translocates a diverse repertoire  of effector proteins either to extracellular locations or directly into eukaryotic cells, in a Sec-independent manner. The T3SS effectors(T3EPs) modulate the function of crucial host regulatory molecules and trigger a range of highly dynamic cellular responses which determine pathogen-host recognition, pathogen/symbiont accommodation and elicitation or suppression of defense responses by the eukaryotic hosts. In some cases however, effector proteins are simply secreted out of the cell. T3SS have evolved into seven families. Some bacteria may harbor more than one T3SS, usually from different families. T3SS genes are encoded in pathogenicity islands and/or are located on plasmids, and are commonly subject to horizontal gene transfer. 

Type IV secretion system: 

In comparison to other secretion systems, T4SS is unique in its ability to transport nucleic acids in addition to proteins into plant and animal cells, as well as into yeast and other bacteria. Usually T4SS comprises 12 proteins that can be identified as homologs of the VirB1–11 and VirD4 proteins of the Agrobacterium tumefaciens Ti plasmid transfer system. T4SS spans both membranes of Gram-negative bacteria, using a specific transglycosylase, VirB1, to digest the intervening murein . While many organisms have homologous type IV secretion systems, not all systems contain the same sets of genes. The only common protein is VirB10 (TrbI) among all T4SS systems. 

Type V secretion system:

T5SS is  the simplest protein secretion mechanism. Proteins are

secreted via the autotransporter system (type Va or AT-1), the two-partner secretion pathway (type Vb), and the oligomeric autotransporters (type Vc or AT-2 system). Proteins secreted via these pathways have similarities in their primary structures as well as striking similarities in their modes of biogenesis.There are three sub-classes of T5SS. The archetypal bacterial proteins secreted via the T5SS (T5aSS subclass) consist of a N-terminal passenger domain of 40-400 kD in size and a conserved C-terminal domain. The proteins are synthesized with a N-terminal signal peptide that directs their export into the periplasm via the Sec machinery. 

Type VI secretion system:

In T6SS 13 genes are thought to constitute the minimal number needed to produce a functional apparatus. TheT6SS gene clusters (T6SS loci) often occur in multiple, non-orthologous  copies per genome and have probably been acquired via horizontal gene transfer. Each T6SS probably assumes a different role in the interactions of the harbouring organism with others. Although the T6SS has been studied primarily  in the context of pathogenic bacteria-host interactions, it has been suggested that it may also function to promote commensal or mutualistic relationships between bacteria and eukaryotes, as well as to mediate cooperative or competitive interactions between bacterial species.  The T6SS machinery constitutes a phage-tail-spike-like injectisome that has the potential to introduce effector proteins directly into the cytoplasm of host cells, analogous to the T3SS and T4SS machineries.

Genetic, structural and biochemical studies of the above bacterial secretion systems along with massive  in silico analyses of microbial genomes have been used to distinguish pathogens from their non-pathogenic relatives. These studies have established the presence of characteristic conserved features within  individual types of secretion systems, along with considerable sequence and structural diversities within each system at the level of specific components and effector proteins.

Despite the complexity of these systems however, the problem of identifying conserved features and properties within each secretion system type, or across several types of systems is of particular importance, going beyond  a fundamental understanding of how bacterial secretion works. Even for well studied pathogens, not all virulence factors have been identified, making it possible that e.g. effector proteins that are associated with different diseases are still unknown. In less well characterized bacterial species there is certainly a wide spectrum of unknown effectors. This  situation may be now changing through new approaches that use advanced machine learning algorithms to identify within individual types of secretion systems common themes for effectors and other system components thatgo beyond simple amino acid motifs), or through the identification of important structural and physicochemical properties as universal signatures of virulence factors.

This review will focus on the well-characterized T3SS proteins where the prevalence of coiled-coil domains along with pronounced structural flexibility/disorder have been proposed to be characteristic properties associated with a protein-protein interaction mode within T3SS and as essential requirements for secretion. Common themes with other secretion systems (T4SS, T6SS) will be also discussed.