Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli

Zerillo, Marcelo M.; Sluys, Marie‐Anne Van; Camargo, L. E. A.; Monteiro-Vitorello, Cláudia Barros

doi:10.1186/1471-2180-8-127

Cited by 12 publications

(6 citation statements)

References 40 publications

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“…Insertion sequence (IS) elements have recently been shown to play a role in plant pathogenicity [ 56 - 59 ]. These elements may inactivate genes on insertion or activate and/or enhance the expression of nearby genes [ 57 , 60 , 61 ]. One characteristic of the Xoo genomes sequenced to date is the accumulation of many IS elements, representing as much as 10% of the Xoo genome size [ 23 ].…”

Section: Resultsmentioning

confidence: 99%

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

et al. 2010

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BackgroundBacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian X. oryzae pv. oryzicola (Xoc).ResultsChanges in gene expression of the African Xoo strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH Xoo DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai) with bacteria grown in vitro. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The Xoo MAI1 non-redundant set of sequences was compared against several X. oryzae genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis.ConclusionsThis is the first report to compare the expression of Xoo genes in planta across different time points during infection. This work shows that as-yet-unidentified and potentially new virulence factors are appearing in an emerging African pathogen. It also confirms that African Xoo strains do differ from their Asian counterparts, even at the transcriptional level.

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Section: Resultsmentioning

confidence: 99%

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

et al. 2010

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“…While the prototypical IS30 element from E. coli carries a single ORF (36), the IS30-like Tpase from ICE6013 is encoded by two ORFs. A two-ORF structure for an IS30-like element, ISLxc4, has also been reported for the plant-inhabiting bacterium Leifsonia xyli, though it was not linked to an ICE (37). Our updated annotation of the IS30-like Tpase indicates that a fusion product of orf1 and orf2 has an N-terminal DNA-binding domain with two putative helix-turn-helix motifs (encoded by orf2) and a C-terminal catalytic domain with the DDE motif (encoded by orf1) (Fig.…”

Section: Discussionmentioning

confidence: 85%

Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus

et al. 2017

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ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus. Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA. The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013. Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013. A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.

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“…cynodontis (previously Clavibacter xyli subsp. cynodontis), the causal agent of ratoon stunting disease in sugarcane (17). In this case, a 41% sequence identity was observed for a stretch of 105 residues.…”

Section: Identification Of the Gene Encoding Cmmamp-i Analysis Of Trmentioning

confidence: 83%

New Type of Antimicrobial Protein Produced by the Plant Pathogen Clavibacter michiganensis subsp. michiganensis

Liu

Holtsmark

et al. 2013

Appl Environ Microbiol

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It has previously been shown that the tomato pathogen Clavibacter michiganensis subsp. michiganensis secretes a 14-kDa protein, C. michiganensis subsp. michiganensis AMP-I (CmmAMP-I), that inhibits growth of Clavibacter michiganensis subsp. sepedonicus, the causal agent of bacterial ring rot of potato. Using sequences obtained from tryptic fragments, we have identified the gene encoding CmmAMP-I and we have recombinantly produced the protein with an N-terminal intein tag. The gene sequence showed that CmmAMP-I contains a typical N-terminal signal peptide for Sec-dependent secretion. The recombinant protein was highly active, with 50% growth inhibition (IC 50 ) of approximately 10 pmol, but was not toxic to potato leaves or tubers. CmmAMP-I does not resemble any known protein and thus represents a completely new type of bacteriocin. Due to its high antimicrobial activity and its very narrow inhibitory spectrum, CmmAMP-1 may be of interest in combating potato ring rot disease.

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Characterization of new IS elements and studies of their dispersion in two subspecies of Leifsonia xyli

Cited by 12 publications

References 40 publications

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus

New Type of Antimicrobial Protein Produced by the Plant Pathogen Clavibacter michiganensis subsp. michiganensis

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