Evolution of Bacterial Protein Secretion

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Slide 1 :

Protein Secretion Systems: Structure and Evolution Milton H. Saier, Jr. Division of Biological Sciences University of California at San Diego La Jolla, CA 92093-0116, USA msaier@ucsd.edu SGM 162nd Meeting - Edinburgh OUTLINE 1, Overview 2, Sec & Tat 3, ABC (I) 4, MTB (II) 5, Fla/Path (III) 6, Conj/Vir (IV) 7, The Big Picture

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Complex Protein Secretion Systems in Gram-negative Bacteria 1, OVERVIEW

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Protein Translocases in Mitochondria

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The topogenesis pathway of ?-barrel membrane proteins is conserved during evolution.

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Gram-negative Bacterial Inner Membrane Channel-forming Protein Translocases

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Gram-negative Bacterial Outer Membrane Channel-forming Protein Translocases

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The General Secretion (Sec) Pathway 2, SEC and TAT Ubiquitous!

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Phylogenetic Tree for SecY/Sec61? Homologues Thien Cao Protein phylogeny = rRNA phylogeny; diversity is greatest in bacteria.

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The Tat System Not Ubiquitous, but wide spread.

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Phylogeny of the TatC homologues Ming Ren Yen Again, no horizontal transfer between phylogenetic groups!

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3, ABC (I)

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ABC Efflux Porters: Topological Types Maxim Dukarevich Bin Wang (Brian) Mirium Khwaja

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ABC1 Nineteen families are known in prokaryotes and eukaryotes. Only ABC1 porters may be present in eukaryotes. These porters are often duplicated and fused to other domains (ABC and Mem) in various orders. They transport all kinds of substrates from simple ions to complex macromolecules. 2 triplicated = 6

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ABC2 Five known ABC2 families are found only in bacteria, but are represented in many bacterial kingdoms. They are never (almost never) duplicated or fused to other domains. These porters export complex carbohydrates: CPS, LOS, LPS and TA, but also drugs. 3 duplicated = 6

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ABC3 Four families are known in bacteria. They are often duplicated and fused to other domains (ABC and Mem), but in non-random arrangements. They transport peptides (e.g., bacterocins), and proteins (e.g., lipoproteins). 4 duplicated = 8 or 10

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ABC3 Topological Types SOMETIMES DUPLICATION GENERATES NEW TMSs!

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Comparisons of MFPs with OMAs MFP (8.A.1) 1. Adaptors, connecting IM ABC, MFS, RND or AAE porters with OMF porins; export proteins, drugs, etc. 2. G- and G+ bacteria 3. 350-450aas; have long coiled coil domains. 4. Span periplasm; C-terminal 6 ?-strand barrel interacts with porter. 5. Form permanent or transient substrate-induced complexes with the porter and OMF. OMA (1.B.18) Adaptors and porins, functioning with ABC or PST porters; exports exo-polysaccharides. G- bacteria only. 350-450aas; have long coiled coil domains. Span periplasm; C-terminal domains form the OM pore. Form complexes with the biosynthetic enzymes, porter, and RhsA at the cell pole.

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Alignment of an OMA with an MFP Anthony Xiao Extensive homology, but only in alpha- proteobacteria.

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Hydropathy and Secondary Structural Predictions for an OMA and an MFP Anthony Xiao

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Comparison of LolA and LolB LolA and LolB are sequence divergent but homologous. They have similar 3D structures. Each has a hydrophobic active site cavity (the opening in an incomplete ?-barrel) plus an ?-helical lid. LolA forms transient complexes with LolCDE and LolB. LolA & B are homologous to LppX of Mycobacteria, an OM lipid (mycolate) insertase. Acyl-CD(KS) is an IM retention signal. LolA: A periplasmic chaperone for LPs. LolB: An OM receptor for LP insertion.

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Pathway for Outer Membrane (OM)Lipoprotein (LP) Export and Insertion Pre-LP (in) Sec; Processing LP (IM, Periplasmic Face) LolCDE ATP LolB•LP (OM Receptor, Integrase) LP (OM) LolA•LP (Periplasmic Chaperone) Min Lee EVOLUTIONARY SEQUENCE DIVERGENCE HAS GENERATED NEW DISSIMIAR FUNCTIONS!

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ABC Uptake Porters: A 5 TMS Topology (Proposed origin from a 2TMS hairpin structure) ABC4: Eric Sun Uptake porters are known only in prokaryotes (with one exception). They can be duplicated and fused to other domains (ABC, Receptor and Membrane) in various orders. They take up all kinds of small biological molecules, and occasionally macromolecules. 2 duplicated = 5

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4, MTB (II)

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Proteins of the Main Terminal Branch (MTB; T2SS) (Related to Type IV Pili and Archaeal Flagella) 14 protein constituents of the transenvelope secreton in Klebsiella pneumoniae 2: An ATPase and its anchor/chaparone 5: Intergral inner memberane/periplasmic proteins 5: Four prepilins, processed by a peptidase/methylase 2: Outer membrane secretin and its anchor/chaparone Toff Peabody

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Phylogenetic tree for ATPases Homologues cluster according to functional type

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Phylogenetic tree for TM homologues Homologues cluster according to functional type but differ from ATPases

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Average Hydropathy Plots for (a) Bacterial and (b) Archaeal TM Homologues Duplication of 2 giving 4 Duplication of 4 giving 8+

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Phylogenetic tree for secretin homologues Secretins are used for many purposes!

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5, FLA/PATH (III)

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Slide 31 :

Phylogenetic trees for six families of TIIIPS-Fla homologues fla & III separated early; frequent lateral transfer; no shuffling

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Evolution of the Bacterial Flagellum Bacterial flagella are modular structures consisting of (1) a basal body, (2) a filamentous propeller, (3) an interconnecting hook complex, (4) a rotary motor, (5) a secretion/assembly system, (6) a secretion energizing ATPase, and (7) various ancillary proteins. Each module probably evolved independently of the others from primordial systems having nothing to do with cell motility. Complexity arose by domain and protein recruitment as well as by intragenic and extragenic duplication events. Hundreds of structurally and functionally distinct flagella, present in various bacterial species, share only about half their protein constituents.

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Homology of six flagellar subunits Alexandra Dodds Sara Siddiqi Tim Wong Arezou Amidi Jing Wang Tracy Yep Dorjee Gyaltsen

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F-type ATPase Some subunits are homologous to flagellar subunits

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6, CONJ/VIR (IV)

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Similarities between T4SS and T6SS Michael Stockin T4SSs are ubiquitous in bacteria, and are extremely diverse in sequence, making identification difficult. They vary in #s of protein constituents, types of constituents, and even transport function.

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7, THE BIG PICTURE!!! PROPOSED EVOLUTIONARY PATHWAY FOR APPEARANCE OF TRANSPORT SYSTEMS

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Slide 39 :

Comparisons of CDF Carriers with Crac Channels CDF (2.A.4) Secondary Carriers: catalyze Me2+:H+ antiport. Ubiquitous; in PM & ICMs of eukaryotes. 6 TMSs; N- and C-termini inside; dimeric. Much size and sequence divergence. Two aspartates are critical for Me2+ binding. Crac-C (1.A.52) Channels: catalyze bidirectional Ca2+ flux. Present only in animals; at PM/ER junctions. 4 TMSs; N- and C-termini inside; tetrameric. Little size and sequence divergence. Two glutamates are critical for Ca2+ binding. Madeline Mathias

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Proposed Common Origin for CRAC channels and CDF carriers Madeline Matias

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The VAP Superfamily of 1? and 2? Transporters Eric Sun BioY has 3 domains encoded by 3 genes. ThiW has 3 domains encoded by 1 gene. They are probably primary active transporters. TrpP consist of a single membrane Domain. (dimers)? PNaS homologues have this domain duplicated. They are secondary carriers.

Slide 42 :

Thank You Vielen Dank(German) T´oo-Je-Che (Tibetan) Kamsa-hamnida (Korean) Shukriya (Hindi) Xie xie (Chinese) Dom?o arigat?o (Japanese) Gracias(Spanish) Merci(French) Ai Yamaguchi Ji-won Youm Jose Marquez John Ehrhart Dorjee Gyaltsen Balaji Sriram Thomas Ballieau Jing Wang

Protein Kinase C iso...

History and Evolutio...

Towards a new model ...

Gonococcal efflux pu...

Nonstructural protei...

ACUTE BACTERIAL MENI...

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	msaier@ucsd.edu 5 Years ago.



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