literature
Table of Contents
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
literature.txt · Last modified: 2023/10/18 13:30 by chk