Research on VgrG Proteins and Phylogeny
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Questions and Answers

What is the main focus of the research described in the text?

  • Examining the role of gene transfer in bacterial evolution.
  • Understanding the mechanisms of bacterial toxin production.
  • Characterizing the diversity of a particular bacterial species.
  • Investigating the evolution of a specific gene cluster involved in a bacterial toxin delivery system. (correct)

    • Based on the text, what is the phylogenetic relationship between G8-G6-G14-G2-G4-G7-G9-G3-G15 and the MRCA (Most Recent Common Ancestor)?

  • G8-G6-G14-G2-G4-G7-G9-G3-G15 are more closely related to the MRCA than any other group.
  • G8-G6-G14-G2-G4-G7-G9-G3-G15 are distantly related to the MRCA.
  • G8-G6-G14-G2-G4-G7-G9-G3-G15 are a direct descendant of the MRCA. (correct)
  • G8-G6-G14-G2-G4-G7-G9-G3-G15 represent a lineage that diverged from the MRCA at a later point.

    • What is the main approach used by the researchers to understand the diversity of VgrG proteins?

  • Studying the protein structure of VgrG variants.
  • Analyzing the genetic sequences of VgrG homologs. (correct)
  • Investigating the interactions of VgrG proteins with other cellular components.
  • Observing the phenotypic differences in bacterial strains with different VgrG types.

    • Which of these statements accurately describes the relationship between domain architecture and phylogeny of VgrG proteins?

    <p>The phylogeny of VgrG proteins based on different domains does not always show the same topology. (B)</p> Signup and view all the answers

    What does the text suggest about the distribution of VgrG variants?

    <p>VgrG variants are found both in the main T6SS gene cluster and in accessory loci. (A)</p> Signup and view all the answers

    How many domains are present in all VgrG variants according to the text?

    <p>3 (A)</p> Signup and view all the answers

    What is the main function of the T6SS gene cluster described in the text?

    <p>To produce toxins for defense against other bacteria. (B)</p> Signup and view all the answers

    What is the significance of the fact that domain 1 of VgrG is the most conserved?

    <p>It suggests that this domain is essential for the function of the T6SS gene cluster. (A)</p> Signup and view all the answers

    What is the main method used to define species within the A. tumefaciens complex?

    <p>Comparison of core gene sequences (A)</p> Signup and view all the answers

    What is the significance of the multimodal distribution of genome similarities shown in Figure 1B?

    <p>It suggests that there are clear genetic barriers between different genomospecies. (A)</p> Signup and view all the answers

    How does the text suggest the A. tumefaciens complex will likely change in the future?

    <p>The diversity within the <em>A. tumefaciens</em> complex will likely increase. (B)</p> Signup and view all the answers

    Based on the text, why is the taxonomy of Agrobacterium complex?

    <p>Because of the variety of plasmids and their associated phenotypes found in <em>Agrobacterium</em>. (D)</p> Signup and view all the answers

    What is the relationship between strain MAFF210266 and strain K599?

    <p>They share 98% ANI, but K599 contains a pRi plasmid causing hairy root disease. (A)</p> Signup and view all the answers

    What is the significance of the vir genes highlighted in Figure 7, and their distribution among genomospecies?

    <p>These genes are responsible for the transfer of T-DNA to plant cells. (D)</p> Signup and view all the answers

    What does the difference in vir gene content among genomospecies suggest?

    <p>All of the above are possible implications. (D)</p> Signup and view all the answers

    What is the main conclusion drawn from the study regarding the A. tumefaciens complex?

    <p>The <em>A. tumefaciens</em> complex is a diverse group of bacteria with significant genetic variation and potential for further discovery. (B)</p> Signup and view all the answers

    What process was used to incorporate gap-filling results in the final assembly?

    <p>PCR and Sanger sequencing (A)</p> Signup and view all the answers

    What was used to run TBLASTN searches for gene confirmation?

    <p>Protein sequences of known genes (B)</p> Signup and view all the answers

    Which version of FastANI was used to calculate pairwise genome similarities?

    <p>FastANI v1.1 (B)</p> Signup and view all the answers

    What criteria were set for the conserved domains identified using MEME?

    <p>Present in at least two sequences (A)</p> Signup and view all the answers

    Which program was mentioned for the visualization of curated results?

    <p>genoPlotR (D)</p> Signup and view all the answers

    What is the acceptable size range for conserved domains as per the MEME criteria?

    <p>30 to 300 a.a. (C)</p> Signup and view all the answers

    What type of genes were manually added back to the T6SS-associated genes list?

    <p>Genes with a e-value above the cutoff (C)</p> Signup and view all the answers

    What was the main focus of the comparative and evolutionary analysis described?

    <p>Pairwise genome similarities and plasmid comparisons (D)</p> Signup and view all the answers

    What method is used to genetically modify plants using Agrobacterium?

    <p>Agrobacterium-mediated transformation (D)</p> Signup and view all the answers

    A. tumefaciens is significant in the field of which of the following disciplines?

    <p>Microbiology (C)</p> Signup and view all the answers

    Which of these species are NOT mentioned as examples of beneficial microbes?

    <p>Vibrio cholerae (C), Pseudomonas aeruginosa (D)</p> Signup and view all the answers

    Which of these methods plays a major role in defining species boundaries in the Agrobacterium complex?

    <p>DNA sequencing (B)</p> Signup and view all the answers

    What is the proposed name for Agrobacterium genomospecies G8?

    <p>Agrobacterium fabrum (C)</p> Signup and view all the answers

    What is the significance of 95% average nucleotide identity (ANI) in bacterial species delineation?

    <p>It indicates close evolutionary relationships between species. (C)</p> Signup and view all the answers

    Based on the text, why is it important to have a consistent understanding of species within Agrobacterium?

    <p>To improve research and development of new crop varieties. (A)</p> Signup and view all the answers

    What is a major obstacle in defining the Agrobacterium species?

    <p>The occurrence of multiple species complexes within the genus. (C)</p> Signup and view all the answers

    What was the total number of aligned amino acid sites analyzed for the two novel pTi sequences?

    <p>15,473 (C)</p> Signup and view all the answers

    What are the virulence (vir) genes indicated by in the gene organization of the vir regulons on pTi?

    <p>Red blocks (D)</p> Signup and view all the answers

    What is the minimum score set for identifying putative T4SS effectors using the T4SEpre tool?

    <p>0.8 (B)</p> Signup and view all the answers

    Which gene type is highlighted in yellow in the vir regulon gene organization on pTi?

    <p>Tra genes (B)</p> Signup and view all the answers

    What type of genes does strain 12D1 harbor related to opine metabolism?

    <p>Transporter genes (B), Catabolism genes (C)</p> Signup and view all the answers

    What was used as a negative control in the tomato tumor assay?

    <p>Sterilized water (C)</p> Signup and view all the answers

    How many core genes were analyzed excluding the two novel pTi?

    <p>40 (B)</p> Signup and view all the answers

    What motif was used to identify putative T-DNA borders?

    <p>YGRCAGGATATATNNNNNKGTMAWN (C)</p> Signup and view all the answers

    What was the constant temperature maintained during the tomato tumorigenesis assays?

    <p>22 °C (B)</p> Signup and view all the answers

    What method was used to confirm the presence of the gene virB7 in the plasmids?

    <p>BLASTN searches (B)</p> Signup and view all the answers

    Which of the following strains had their virulence evaluated during the assays?

    <p>Known-You 301 (D)</p> Signup and view all the answers

    What type of sequencing service was provided by Genomics BioSci & Tech Co. Ltd.?

    <p>PacBio sequencing (A)</p> Signup and view all the answers

    Which growth regime was maintained for the plants used in the assays?

    <p>16-/8-h light/dark regime (A)</p> Signup and view all the answers

    Which organization issued the permits for importing the bacterial strains?

    <p>Council of Agriculture of Taiwan (B)</p> Signup and view all the answers

    What type of technical assistance was acknowledged in the study?

    <p>Technical assistance with experiments (A)</p> Signup and view all the answers

    What is the potential implication of homologous recombination in Agrobacterium as mentioned?

    <p>Affects genomic species concept in bacteria (C)</p> Signup and view all the answers

    Flashcards

    Agrobacterium-mediated transformation

    A method for genetic manipulation in plants using Agrobacterium.

    Bacterial species complexes

    Groups of closely related bacteria with genetic diversity needing classification.

    Genomic information

    Data regarding the complete genetic makeup of an organism.

    Genomospecies

    Distinct biological entities defined by overall genome divergence.

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    Nucleotide identity

    The measure of similarity between DNA sequences.

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    Phenotypic diversity

    Variations in observable traits among organisms.

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    Taxonomy

    The science of classifying and naming organisms.

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    Heterotypic synonym

    Different names referring to the same taxonomic entity.

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    T6SS gene cluster

    A group of genes involved in the type VI secretion system, associated with bacterial interaction.

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    MRCA

    Most Recent Common Ancestor, the latest common ancestor in a group of organisms.

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    Gene co-occurrence

    When two or more genes are found together in an organism or group.

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    VgrG proteins

    Proteins associated with T6SS that can vary in domain structure and function.

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    Phylogeny

    The study of evolutionary relationships among biological entities.

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    Domain architecture

    The arrangement and composition of functional regions within a protein.

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    Homologs

    Genes or proteins that share a common ancestry but may have different functions.

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    Monophyletic groups

    Groups of organisms that consist of a common ancestor and all its descendants.

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    Agrobacterium taxa

    A grouping of related bacterial species, particularly Agrobacterium species.

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    Core gene sequences

    The essential genes shared among related species, used for classification.

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    ANI

    Average Nucleotide Identity, a method for comparing genomic sequences between bacteria.

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    T4SS

    Type IV secretion system, important for transferring proteins and DNA in bacteria.

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    Vir genes

    Genes associated with virulence in Agrobacterium that aid in infection.

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    Plasmid pRi

    A root-inducing plasmid in Agrobacterium linked to hairy root disease.

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    Agrobacterium rhizogenes

    A species of Agrobacterium known for causing hairy root disease in plants.

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    DUF4123 domain

    A protein domain associated with certain gene functions, linked to T6SS chaperones.

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    NCBI

    The National Center for Biotechnology Information that provides genomic data and resources.

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    TBLASTN

    A bioinformatics tool that compares nucleotide sequences against a protein database.

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    FastANI

    A tool for calculating Average Nucleotide Identity across genomes efficiently.

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    Syntenic regions

    Conserved segments of genomes that maintain their order across different species.

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    Gene content comparison

    The analysis of the presence and arrangement of genes between different genomes.

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    MEME v5.1.1

    Software used to identify conserved motifs in a set of sequences.

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    virA/J

    Genes located on a plasmid important for tumorigenesis in plants.

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    Tumorigenesis assay

    Test to evaluate the ability of bacteria to induce tumors in plants.

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    Inoculation in plants

    The process of introducing bacteria into plant tissues for study or treatment.

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    pTiChry5

    A specific plasmid associated with Agrobacterium species affecting tumorigenesis.

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    BLASTN searches

    A tool used to compare nucleotide sequences and confirm gene presence.

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    Agrobacterium strains

    Different varieties of bacteria that can induce tumors in plants.

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    Illumina sequencing

    A high-throughput method for sequencing DNA, widely used in genomics.

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    Type VI secretion system (T6SS)

    A complex of proteins bacteria use to transport effector molecules to other cells.

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    pTi typing

    A classification method for oncogenic plasmids based on k-mer profile clustering.

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    T-DNA identification

    The process of identifying transfer DNA regions based on specific motifs.

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    Opine metabolism

    Biochemical processes in plants that involve opines, often manipulated by Agrobacterium.

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    T4SS effectors

    Proteins secreted by a type IV secretion system involved in bacterial virulence.

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    Virulence genes

    Genes responsible for the ability of a pathogen to cause disease.

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    Conjugation genes

    Genes involved in the transfer of genetic material between bacteria through direct contact.

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    Bootstrap support

    A statistical method that estimates the reliability of phylogenetic trees.

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    Study Notes

    Modular Evolution of Secretion Systems and Virulence Plasmids in a Bacterial Species Complex

    • Many bacterial species are part of complexes, making genetic diversity research challenging.
    • Agrobacterium tumefaciens, a plant pathogen, was used to study species complexes.
    • 35 genome assemblies, including 14 new ones, were used to understand diversity.
    • Previous 10 genomospecies were found distinct biological species.
    • A quantitative guideline was developed for identifying bacterial species.
    • Genes crucial for fitness and ecology were investigated.
    • The type VI secretion system (T6SS) had multiple losses and one horizontal gene transfer.
    • Tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion systems (T4SS) have diverse forms.
    • Structural components of T6SS and T4SS are highly conserved.
    • Effectors and other proteins show extensive diversity.
    • Phylogeny-guided sampling and high-quality genome assemblies are key for robust evolutionary genomics.
    • Protein VgrG involved in effector binding and delivery can be categorized into distinct types based on its domain organization.
    • Patterns of co-occurrence of VgrG and associated genes suggest possible interacting partners.
    • Gene and domain modularity is useful in understanding functions, especially in bacteria like Agrobacterium.

    Genome Sampling, Molecular Phylogeny, and Divergence

    • 12 strains and 2 Agrobacterium larrymoorei strains were selected for whole-genome sequencing.
    • This expanded sampling provided an improved view of genetic diversity.
    • A core genome of 2093 single-copy genes was identified, representing 40% annotated genes.
    • Higher core gene count allowed better resolution of the phylogeny.
    • 10 existing genomospecies form distinct monophyletic clades with high bootstrap support (over 80%).
    • Two novel genomospecies (G21 and G22) were identified.
    • Species delineation using 95% ANI cutoff is supported.
    • The common ancestor of the species complex emerged ~ 48 million years ago.

    Diversity and Evolution of T6SS Genes

    • T6SS genes show a patchy distribution.
    • Gene absences were found in under-characterized genomospecies.
    • T6SS-encoded genes are often clustered in the linear chromosomes.
    • A diverse set of effector and immunity (EI) proteins were identified.
    • Extensive diversity exists in VgrG domains influencing effector binding specificities.

    Diversity and Evolution of Virulence Plasmids

    • 15 tumor-inducing plasmids (pTi) were identified.
    • Two novel putative pTi were discovered (pTiCFBP4996 and pTiCFBP5473).
    • Genetic variations exist in pTi, including T-DNA sizes, gene organization, and vir regulon gene distribution.

    Discussion and Conclusions

    • 95% ANI is a strong species boundary measure.
    • The high DNA divergence among closely related Agrobacterium species was highlighted.
    • The combination of phylogenetics and genomics is crucial for understanding bacterial species complexes.
    • The complex modular structure of bacterial genomes shows adaptive features in their evolution.
    • This comprehensive study improves the understanding of bacterial species organization, diversity, and evolutionary relationships.

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    Modular Evolution of Secretion Systems and Virulence Plasmids in Agrobacterium PDF

    Description

    This quiz explores the main findings from the research on VgrG proteins, focusing on their phylogenetic relationships and domain architectures. It delves into methods used to analyze diversity, the significance of conserved domains, and predictions about the future of the A. tumefaciens complex. Test your understanding of these complex topics related to microbiology and molecular biology.

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