Agrobacteria-Rhizobia Complex

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====== Literature ======


===== Review =====
  * Kado (2014) Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by //Agrobacterium tumefaciens//. Front Microbiol. 5:340. [[https://doi.org/10.3389/fmicb.2014.00340]]
  * Nester (2015) //Agrobacterium//: nature’s genetic engineer. Front Plant Sci 5:730. [[https://doi.org/10.3389/fpls.2014.00730]]
  * Hwang et al. (2017) //Agrobacterium//-mediated plant transformation: biology and applications. Arabidopsis Book 15:e0186. [[https://doi.org/10.1199/tab.0186]]
  * Hooykaas (2023) The Ti plasmid, driver of Agrobacterium pathogenesis. Phytopathology 113:594–604. [[https://doi.org/10.1094/PHYTO-11-22-0432-IA]]
  * Weisberg et al. (2023) Virulence and ecology of agrobacteria in the context of evolutionary genomics. Annu Rev Phytopathol. 61:1-23. [[https://doi.org/10.1146/annurev-phyto-021622-125009]]

===== Genomospecies =====
  * Popoff et al. (1984) Position taxonomique de souches de Agrobacterium d’origine hospitalière. Ann Inst Pasteur Microbiol 135, 427–442. [[https://doi.org/10.1016/S0769-2609(84)80083-6]]
    * Classification of agrobacteria into distinct groups (i.e., genomospecies) based on phenotype and overall genome similarity (DNA-DNA hybridization)
  * Costechareyre et al. (2010). Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity. Microb Ecol 60:862–872. [[https://doi.org/10.1007/s00248-010-9685-7]]
  * Lassalle et al. (2011). Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol 3:762–781. [[https://doi.org/10.1093/gbe/evr070]]
    * Use strain C58 (BV1 G8) as the reference, performed microarray hybridization to check presence/absence of specific genomic regions in 25 different strains; strains classified to the same genomospecies are more similar.
    * G8 named as //Agrobacterium fabrum//
  * Shams et al. (2013). Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR. Syst Appl Microbiol 36:351–358. [[https://doi.org/10.1016/j.syapm.2013.03.002]]
  * Lassalle et al. (2017) Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium. Genome Biol Evol 9, 3413–3431. [[https://doi.org/10.1093/gbe/evx255]]
  * Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. [[https://doi.org/10.1126/science.aba5256]]
    * Large-scale ANI analysis
  * Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. [[https://doi.org/10.1186/s12915-021-01221-y]]
    * Genome-scale phylogeny; comparison of divergence based on average nucleotide identity (ANI) and gene content; focused analysis on secretion systems and plasmids



===== Genome =====
  * Goodner et al. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323–2328. [[https://doi.org/10.1126/science.1066803]]
  * Wood et al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317–2323. [[https://doi.org/10.1126/science.1066804]]
    * Goodner et al. (2001) and Wood et al. (2001) are back-to-back papers; first //Agrobacterium// genome sequence, strain C58
  * Slater et al. (2009) Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191:2501–2511. [[https://doi.org/10.1128/JB.01779-08]]
    * The first genome sequence for BV2 (strain K84) and BV3 (strain S4); 3-way comparison with BV1 (C58)
    * Model for the evolution of different chromosome/chromid organization among different lineages of ARC
  * Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. [[https://doi.org/10.1126/science.aba5256]]
    * Large scale genome sequencing; ??? new assemblies released
  * Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. [[https://doi.org/10.1186/s12915-021-01221-y]]
    * Major improvement in the taxon sampling; 14 (nearly) complete assemblies from genomospecies that were poorly characterized



===== Chromid =====
  * Harrison et al. (2010) Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid. Trends Microbiol 18:141–148. [[https://doi.org/10.1016/j.tim.2009.12.010]]
    * Opinion paper on the concept of chrmoid
  * Ramírez-Bahena et al. (2014) Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Mol Phylogenet Evol 73:202–207. [[https://doi.org/10.1016/j.ympev.2014.01.005]]
    * Strains with a linear chromid shared a common ancestor, which acquired telA [[https://doi.org/10.1016/j.ympev.2014.01.005]]



===== Plasmids =====
  * Gordon and Christie (2014). The Agrobacterium Ti plasmids. Microbiol Spectr 2, 2.6.19. [[https://doi.org/10.1128/microbiolspec.PLAS-0010-2013]]
  * Weisberg et al. (2020). Unexpected conservation and global transmission of agrobacterial virulence plasmids. Science 368:eaba5256. [[https://doi.org/10.1126/science.aba5256]]
  * Weisberg et al. (2022) Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria. Philos Trans R Soc Lond B Biol Sci 377, 20200466. [[https://doi.org/10.1098/rstb.2020.0466]]



===== Type IV Secretion System (T4SS) =====



===== Type VI Secretion System (T6SS) =====
  * Many, but not all, species within the agrobacteria-rhizobia complex have a conserved gene cluster that encode the T6SS. This system is involved in interbacterial competition.

  * Lin et al. (2013) Systematic dissection of the Agrobacterium type VI secretion system reveals machinery and secreted components for subcomplex formation. PLOS ONE 8, e67647. [[https://doi.org/10.1371/journal.pone.0067647]]
  * Lin et al. (2014). Fha Interaction with Phosphothreonine of TssL Activates Type VI Secretion in Agrobacterium tumefaciens. PLOS Pathog 10, e1003991. [[https://doi.org/10.1371/journal.ppat.1003991]]
  * Ma et al. (2014) Agrobacterium tumefaciens deploys a superfamily of type VI secretion DNase effectors as weapons for interbacterial competition in planta. Cell Host Microbe 16, 94–104. [[https://doi.org/10.1016/j.chom.2014.06.002]]
  * Wu et al. (2019) Plant-pathogenic Agrobacterium tumefaciens strains have diverse type VI effector-immunity pairs and vary in in-planta competitiveness. Mol Plant Microbe Interact 32, 961–971. [[https://10.1094/MPMI-01-19-0021-R]]
  * Wu et al. (2021) Diversification of the type VI secretion system in agrobacteria. mBio 12, e01927-21. [[https://10.1128/mBio.01927-21]]
  * Chou et al. (2022). Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biol 20:16. [[https://doi.org/10.1186/s12915-021-01221-y]]
    * Molecular evolution of the T6SS genes in BV1; diversity of effector genes.



===== Transcriptome =====
  * Haryono et al. (2019) Differentiations in gene content and expression response to virulence induction between two Agrobacterium strains. Front Microbiol 10, 1554. [[https://doi.org/10.3389/fmicb.2019.01554]]
  * Waldburger et al. (2023) Transcriptome architecture of the three main lineages of agrobacteria. mSystems 8, e00333-23. [[https://doi.org/10.1128/msystems.00333-23]]


===== Transformation =====
  * AMT: //Agrobacterium//-Mediated Transformation; Agrobacteria-Mediated Transformation

===== Host Range =====
  * Hwang et al. (2013) Characterization and host range of five tumorigenic Agrobacterium tumefaciens strains and possible application in plant transient transformation assays. Plant Pathol 62, 1384–1397. [[https://doi.org/10.1111/ppa.12046]]


===== Microbiota =====
  * Faist et al. (2016) Grapevine (Vitis vinifera) crown galls host distinct microbiota. Appl Environ Microbiol 82, 5542–5552. [[https://doi.org/10.1128/AEM.01131-16]]
  * Wang et al. (2023) Soil inoculation and blocker-mediated sequencing show effects of the antibacterial T6SS on agrobacterial tumorigenesis and gallobiome. mBio 14, e00177-23. [[https://doi.org/10.1128/mbio.00177-23]]