scholarly journals Host-adaptation in Legionellales is 2.4 Ga, coincident with eukaryogenesis

2019 ◽  
Author(s):  
Eric Hugoson ◽  
Tea Ammunét ◽  
Lionel Guy
Keyword(s):  
Common Ancestor ◽  
Gene Families ◽  
Host Adaptation ◽  
Effector Proteins ◽  
Host Cells ◽  
Eukaryotic Cells ◽  
Last Eukaryotic Common Ancestor ◽  
Molecular Machinery ◽  
Type Ivb Secretion ◽  
Bacterial Clade

AbstractBacteria adapting to living in a host cell caused the most salient events in the evolution of eukaryotes, namely the seminal fusion with an archaeon 1, and the emergence of both the mitochondrion and the chloroplast 2. A bacterial clade that may hold the key to understanding these events is the deep-branching gammaproteobacterial order Legionellales – containing among others Coxiella and Legionella – of which all known members grow inside eukaryotic cells 3. Here, by analyzing 35 novel Legionellales genomes mainly acquired through metagenomics, we show that this group is much more diverse than previously thought, and that key host-adaptation events took place very early in its evolution. Crucial virulence factors like the Type IVB secretion (Dot/Icm) system and two shared effector proteins were gained in the last Legionellales common ancestor (LLCA), while many metabolic gene families were lost in LLCA and its immediate descendants. We estimate that LLCA lived circa 2.4 Ga ago, predating the last eukaryotic common ancestor (LECA) by at least 0.5 Ga 4. These elements strongly indicate that host-adaptation arose only once in Legionellales, and that these bacteria were using advanced molecular machinery to exploit and manipulate host cells very early in eukaryogenesis.

scholarly journals LcrG is Required for Efficient Translocation ofYersinia Yop Effector Proteins into Eukaryotic Cells

1998 ◽  
Vol 66 (6) ◽  
pp. 2976-2979 ◽  
Author(s):  
Mahfuzur R. Sarker ◽  
Marie-Paule Sory ◽  
Aoife P. Boyd ◽  
Maite Iriarte ◽  
Guy R. Cornelis
Keyword(s):  
Immune System ◽  
Yersinia Enterocolitica ◽  
Effector Proteins ◽  
Host Cells ◽  
Eukaryotic Cells

ABSTRACT Extracellular Yersinia disables the immune system of its host by injecting effector Yop proteins into host cells. We show that a Yersinia enterocolitica nonpolar lcrGmutant is severely impaired in the translocation of YopE, YopH, YopM, YpkA/YopO, and YopP into eukaryotic cells. LcrG is thus required for efficient internalization of all the known Yop effectors.

scholarly journals Evolution of late steps in exocytosis: conservation, specialization

2019 ◽  
Vol 4 ◽  
pp. 112
Author(s):  
Cordula Boehm ◽  
Mark C. Field
Keyword(s):  
Structure Prediction ◽  
Common Ancestor ◽  
Sequence Data ◽  
Gene Families ◽  
Sequence Evolution ◽  
Endomembrane System ◽  
Last Eukaryotic Common Ancestor ◽  
Exocyst Complex ◽  
Genes Encoding ◽  
Specific Proteins

Background: The eukaryotic endomembrane system likely arose via paralogous expansion of genes encoding proteins specifying organelle identity, coat complexes and government of fusion specificity. While the majority of these gene families were established by the time of the last eukaryotic common ancestor (LECA), subsequent evolutionary events molded these systems, likely reflecting adaptations retained for increased fitness. As well as sequence evolution, these adaptations include loss of otherwise canonical subunits, emergence of lineage-specific proteins and paralog expansion. The exocyst complex is involved in late exocytosis, and possibly additional pathways, and is a member of the complexes associated with tethering containing helical rods (CATCHR) tethering complex family, which includes conserved oligomeric Golgi (COG), homotypic fusion and vacuole protein sorting (HOPS), class C core vacuole/endosome tethering (CORVET) and others. The exocyst is integrated into a complex GTPase signaling network in animals, fungi and other lineages. Prompted by discovery of Exo99, a non-canonical subunit in the excavate protist Trypanosoma brucei, and significantly increased genome sequence data, we examined evolution of the exocyst. Methods: We examined evolution of the exocyst by comparative genomics, phylogenetics and structure prediction. Results: The exocyst is highly conserved, but with substantial losses of subunits in the Apicomplexa and expansions in Streptophyta plants and Metazoa. Significantly, few taxa retain a partial complex, suggesting that, in the main, all subunits are required for functionality. Further, the ninth exocyst subunit Exo99 is specific to the Euglenozoa with a distinct architecture compared to the other subunits and which possibly represents a coat system. Conclusions: These data reveal a remarkable degree of evolutionary flexibility within the exocyst complex, suggesting significant diversity in exocytosis mechanisms.

scholarly journals Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes

2020 ◽  
Vol 12 (12) ◽  
pp. 2196-2210
Author(s):  
Agnes K M Weiner ◽  
Mario A Cerón-Romero ◽  
Ying Yan ◽  
Laura A Katz
Keyword(s):  
Common Ancestor ◽  
Regulation Of Gene Expression ◽  
Rapid Evolution ◽  
Chromatin Modification ◽  
Gene Families ◽  
Testate Amoebae ◽  
Model Organisms ◽  
Last Eukaryotic Common Ancestor ◽  
Evolutionary Patterns ◽  
Protein Coding

Abstract Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes and evaluate their macroevolutionary patterns among eukaryotes. In addition to data from GenBank, we increase taxon sampling from understudied clades of SAR (Stramenopila, Alveolata, and Rhizaria) and Amoebozoa by adding new single-cell transcriptomes from ciliates, foraminifera, and testate amoebae. We focus on 118 gene families, 94 involved in chromatin modification and 24 involved in non-protein-coding RNA processes based on the epigenetics literature. Our results indicate 1) the presence of a large number of epigenetic gene families in the last eukaryotic common ancestor; 2) differential conservation among major eukaryotic clades, with a notable paucity of genes within Excavata; and 3) punctate distribution of epigenetic gene families between species consistent with rapid evolution leading to gene loss. Together these data demonstrate the power of taxon-rich phylogenomic studies for illuminating evolutionary patterns at scales of >1 billion years of evolution and suggest that macroevolutionary phenomena, such as genome conflict, have shaped the evolution of the eukaryotic epigenetic toolkit.

scholarly journals The extracellular association of the bacterium “CandidatusDeianiraea vastatrix” with the ciliateParameciumsuggests an alternative scenario for the evolution ofRickettsiales

2018 ◽  
Author(s):  
M. Castelli ◽  
E. Sabaneyeva ◽  
O. Lanzoni ◽  
N. Lebedeva ◽  
A.M. Floriano ◽  
...  
Keyword(s):  
Amino Acids ◽  
Common Ancestor ◽  
Genome Reduction ◽  
Host Cells ◽  
Eukaryotic Cells ◽  
Last Common Ancestor ◽  
Human Pathogens ◽  
Alternative Scenario ◽  
Genomic Analyses ◽  
Open Debate

AbstractRickettsialesare a lineage of obligatorily intracellularAlphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novelRickettsialesbacterium associated withParamecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesize amino acids, compared to all investigatedRickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction ofRickettsialesbacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity inRickettsiales. According to our reconstruction, theRickettsialesancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity and genome reduction would have evolved later in parallel and independently in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria withinAlphaproteobacteria.

scholarly journals Evolution and diversification of the nuclear pore complex

2021 ◽  
Author(s):  
Alexandr A. Makarov ◽  
Norma E. Padilla-Mejia ◽  
Mark C. Field
Keyword(s):  
Transport System ◽  
Nuclear Pore Complex ◽  
Common Ancestor ◽  
Mrna Export ◽  
Intraflagellar Transport ◽  
Eukaryotic Cells ◽  
Nuclear Pore ◽  
Last Eukaryotic Common Ancestor ◽  
Structural Characterisation ◽  
Evolutionary Origins

The nuclear pore complex (NPC) is responsible for transport between the cytoplasm and nucleoplasm and one of the more intricate structures of eukaryotic cells. Typically composed of over 300 polypeptides, the NPC shares evolutionary origins with endo-membrane and intraflagellar transport system complexes. The modern NPC was fully established by the time of the last eukaryotic common ancestor and, hence, prior to eukaryote diversification. Despite the complexity, the NPC structure is surprisingly flexible with considerable variation between lineages. Here, we review diversification of the NPC in major taxa in view of recent advances in genomic and structural characterisation of plant, protist and nucleomorph NPCs and discuss the implications for NPC evolution. Furthermore, we highlight these changes in the context of mRNA export and consider how this process may have influenced NPC diversity. We reveal the NPC as a platform for continual evolution and adaptation.

scholarly journals Structural insights into the roles of the IcmS–IcmW complex in the type IVb secretion system of Legionella pneumophila

2017 ◽  
Vol 114 (51) ◽  
pp. 13543-13548 ◽  
Author(s):  
Jianpo Xu ◽  
Dandan Xu ◽  
Muyang Wan ◽  
Li Yin ◽  
Xiaofei Wang ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Hydrophobic Surface ◽  
Adaptor Proteins ◽  
Secretion System ◽  
Effector Proteins ◽  
Host Cells ◽  
Binary Complex ◽  
Type Iv ◽  
Type Ivb Secretion ◽  
Type Ivb Secretion System

The type IVb secretion system (T4BSS) of Legionella pneumophila is a multiple-component apparatus that delivers ∼300 virulent effector proteins into host cells. The injected effectors modulate host cellular processes to promote bacterial infection and proliferation. IcmS and IcmW are two conserved small, acidic adaptor proteins that form a binary complex to interact with many effectors and facilitate their translocation. IcmS and IcmW can also interact with DotL, an ATPase of the type IV coupling protein complex (T4CP). However, how IcmS–IcmW recognizes effectors, and what the roles of IcmS–IcmW are in T4BSSs are unclear. In this study, we found that IcmS and IcmW form a 1:1 heterodimeric complex to bind effector substrates. Both IcmS and IcmW adopt new structural folds and have no structural similarities with known effector chaperones. IcmS has a compact global structure with an α/β fold, while IcmW adopts a fully α-folded, relatively loose architecture. IcmS stabilizes IcmW by binding to its two C-terminal α-helices. Photocrosslinking assays revealed that the IcmS–IcmW complex binds its cognate effectors via an extended hydrophobic surface, which can also interact with the C terminus of DotL. A crystal structure of the DotL–IcmS–IcmW complex reveals extensive and highly stable interactions between DotL and IcmS–IcmW. Moreover, IcmS–IcmW recruits LvgA to DotL and assembles a unique T4CP. These data suggest that IcmS–IcmW also functions as an inseparable integral component of the DotL–T4CP complex in the bacterial inner membrane. This study provides molecular insights into the dual roles of the IcmS–IcmW complex in T4BSSs.

scholarly journals Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Plinio S. Vieira ◽  
Isabela M. Bonfim ◽  
Evandro A. Araujo ◽  
Ricardo R. Melo ◽  
Augusto R. Lima ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Model Organism ◽  
Citrus Canker ◽  
Effector Proteins ◽  
Glycoside Hydrolases ◽  
Host Cells ◽  
System A ◽  
Enzymatic Machinery

AbstractXyloglucans are highly substituted and recalcitrant polysaccharides found in the primary cell walls of vascular plants, acting as a barrier against pathogens. Here, we reveal that the diverse and economically relevant Xanthomonas bacteria are endowed with a xyloglucan depolymerization machinery that is linked to pathogenesis. Using the citrus canker pathogen as a model organism, we show that this system encompasses distinctive glycoside hydrolases, a modular xyloglucan acetylesterase and specific membrane transporters, demonstrating that plant-associated bacteria employ distinct molecular strategies from commensal gut bacteria to cope with xyloglucans. Notably, the sugars released by this system elicit the expression of several key virulence factors, including the type III secretion system, a membrane-embedded apparatus to deliver effector proteins into the host cells. Together, these findings shed light on the molecular mechanisms underpinning the intricate enzymatic machinery of Xanthomonas to depolymerize xyloglucans and uncover a role for this system in signaling pathways driving pathogenesis.

Mammalian mitochondrial translation — revealing consequences of divergent evolution

2019 ◽  
Vol 47 (5) ◽  
pp. 1429-1436 ◽  
Author(s):  
Rawaa A. Z. Al-Faresi ◽  
Robert. N. Lightowlers ◽  
Zofia M. A. Chrzanowska-Lightowlers
Keyword(s):  
Common Ancestor ◽  
Current Knowledge ◽  
Eukaryotic Cells ◽  
Divergent Evolution ◽  
Mitochondrial Translation ◽  
Complete Understanding ◽  
Genetic Origin ◽  
Cryo Electron Microscopy ◽  
Encoded Proteins ◽  
Molecular Aspects

Abstract Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.

scholarly journals Perturbation of host autophagy by the Irish potato famine pathogen

2014 ◽  
Vol 70 (a1) ◽  
pp. C826-C826
Author(s):  
Abbas Maqbool ◽  
Richard Richard ◽  
Tolga Bozkurt ◽  
Yasin Dagdas ◽  
Khaoula Belhai ◽  
...  
Keyword(s):  
Host Cell ◽  
Plant Cells ◽  
Irish Potato ◽  
Effector Proteins ◽  
Host Cells ◽  
Cell Physiology ◽  
Biochemical Basis ◽  
The Impact ◽  
Potato Famine ◽  
Irish Potato Famine

Autophagy is a catabolic process involving degradation of dysfunctional cytoplasmic components to ensure cellular survival under starvation conditions. The process involves formation of double-membrane vesicles called autophagosomes and delivery of the inner constituents to lytic compartments. It can also target invading pathogens, such as intracellular bacteria, for destruction and is thus implicated in innate immune pathways [1]. In response, certain mammalian pathogens deliver effector proteins into host cells that inhibit autophagy and contribute to enabling parasitic infection [2]. Pyhtophthora infestans, the Irish potato famine pathogen, is a causative agent of late blight disease in potato and tomato crops. It delivers a plethora of modular effector proteins into plant cells to promote infection. Once inside the cell, RXLR-type effector proteins engage with host cell proteins, to manipulate host cell physiology for the benefit of the pathogen. As plants lack an adaptive immune system, this provides a robust mechanism for pathogens to circumvent host defense. PexRD54 is an intracellular RXLR-type effector protein produced by P. infestans. PexRD54 interacts with potato homologues of autophagy protein ATG8 in plant cells. We have been investigating the structural and biochemical basis of the PexRD54/ATG8 interaction in vitro. We have purified PexRD54 and ATG8 independently and in complex from E. coli. Using protein/protein interaction studies we have shown that PexRD54 binds ATG8 with sub-micromolar affinity. We have also determined the structure of PexRD54 in the presence of ATG8. This crystal structure provides key insights into how the previously reported WY-fold of oomycete RXLR-type effectors [3] can be organized in multiple repeats. The structural data also provides insights into the interaction between PexRD54 and ATG8, suggesting further experiments to understand the impact of this interaction on host cell physiology and how this benefits the pathogen.

Evolution of vacuolar H+-ATPases: immunological relationships of the nucleotide-binding subunits

1989 ◽  
Vol 67 (6) ◽  
pp. 306-310 ◽  
Author(s):  
Morris F. Manolson ◽  
Judith M. Percy ◽  
David K. Apps ◽  
Xiao-Song Xie ◽  
Dennis K. Stone ◽  
...  
Keyword(s):  
Anaerobic Bacterium ◽  
Common Ancestor ◽  
Sequence Data ◽  
Structural Features ◽  
Eukaryotic Cells ◽  
Clostridium Pasteurianum ◽  
Chromaffin Granules ◽  
Α Subunit ◽  
Evolutionary Origins ◽  
Vacuolar Membranes

The evolution of the endomembrane systems of eukaryotic cells can be examined by exploring the evolutionary origins of the endomembrane H+-ATPases. Recent studies suggest that certain polypeptides are common to all H+ pumps of this type. Tonoplast H+ -ATPase from Beta vulgaris L. was purified and antibodies raised to two of its subunits. Each of these antisera reacted with a polypeptide of the corresponding size in bovine chromaffin granules, bovine clathrincoated vesicles, and yeast vacuolar membranes, suggesting common structural features and a common ancestor for endomembrane H+-ATPases of different organelles and different kingdoms. The antiserum raised against the 57-kDa polypeptide of plant tonoplast H+ -ATPase also reacted with subunit "a" of the H+-ATPase from the obligately anaerobic bacterium Clostridium pasteurianum and to the α subunit of the H+ -ATPase from Escherichia coli. There was no reactivity with chloroplast or mitochondrial ATPases. These results are discussed in relation to recent sequence data which suggest that endomembrane H+-ATPases may be evolutionarily related to the F0F1 ATPases.Key words: H+ -ATPase, evolution, immunology, vacuole, endomembrane.

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