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Chapter 11 : Function, Evolution, and Classification of Macromolecular Transport Systems
Category: Bacterial Pathogenesis; Microbial Genetics and Molecular Biology
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This chapter proposes a universal classification scheme for macromolecular transport systems based on the phylogeny of genes involved in transport and the sequence of events that led to the construction of each system. It focuses on the systems of gram-negative proteobacteria and their relatives in other prokaryotes and eukaryotes. The chapter concentrates on the terminal branches of the sec system along with the sec-independent transporters. It lays out current functional models and discusses evolutionary evidence and hypotheses for eight overarching types, making note of classification disagreements where appropriate. The chapter talks about on the type I secretion: the ATP-binding cassette transporters, type II secretion: the main terminal branch, type III secretion: contact-dependent systems, type IV secretion: conjugation- related systems, and type V secretion: the autotransporters, the chaperone/usher pathway, the alternate chaperone/ usher pathway, and the extracellular nucleation- precipitation pathway. In this chapter, the term "homology" is used to mean "similarity because of common ancestry". Thus, homology is always based on a hypothesis of common ancestry. Many studies presented in this chapter use tree-building techniques such as neighbor joining, which base the branching pattern of tree topology on measurements of aggregate sequence similarities. Confusion surrounding the classification of macromolecular transport systems is based on the lack of a standardized, logical, and systematic basis for nomenclature. Phylogenetic models can be put to work for investigation as good predictors of function that allow reasonable hypotheses to be generated and tested. In addition, many classification disagreements could be clarified by using an explicit and systematic phylogenetic system.
Schematic representations of secretion systems. Symbols indicate established homologous relationships between genes for the proteins pictured. Putative NTPases from the pulE/virB11 superfamily are given single and double daggers. Single daggers indicate putative NTPases from the type II secretion family, and type IV secretion family NTPases are indicated by double daggers. Flagellar apparatuses and type IV pilus systems are grouped with their close relatives. See text for details.
Functional reconstruction of type II and IV secretion using simple Fitch optimization and the virB11/pulE superfamily phylogeny. (A) Reconstruction of substrate evolution. Shades and patterns indicate conjugation (gray);DNA uptake (hatched);and protein secretion, including pilin and flagellar subunits (black). In cases in which two functions have been observed, DNA transport (either conjugation or uptake) is shown. (B) Evolutionary reconstruction of surface organelles: cyclized/thick conjugative pili (black), type IV pili (gray), archaeal flagella (hatched), or no surface structure observed (checked). Trees are derived from the NTPase phylogeny done in this study and are pruned to include better studied taxa. They are rooted with the uncharacterized archaeal NTPases as in reference 136 .
Hypothetical reticulogram for secretion systems. Each line represents a different gene phylogeny. Primary (1°) and secondary (2°) gene associations that could form the basis of a classification system are shown. Type B is defined by a new association between a light gray gene and a black gene after the loss of the dashed gene. Thus, this is defined as a new type independent of type C. Type D can be divided into two subgroups based on the presence or absence of a light gray gene.
Properties of macromolecular transport systems a