A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives

Naushad, Sohail; Adeolu, Mobolaji; Wong, Shirley; Sohail, Misbah; Schellhorn, Herbert E.; Gupta, Radhey S.

doi:10.1007/s10482-014-0344-8

Cited by 136 publications

(67 citation statements)

References 55 publications

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“…oryzicola and X. translucens . Although not otherwise closely related (Naushad et al, 2015), these nominally enter via stomata and propagate throughout the mesophyll parenchyma, causing leaf streak disease, in small grain cereals and forage grasses from a sub-set of the Poaceae /grass plant family, specifically the BEP clade (GPWGII, 2012). However, these plants have highly water-repellent leaves (Neinhuis and Barthlott, 1997), a function of their vertical/upright nature and hydrophobic surface (Koch et al, 2008), which limits bacterial colonization and stomatal access (Beattie, 2011).…”

Section: Discussionmentioning

confidence: 99%

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Nagel

Peters

2017

MPMI

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Summary Certain plant-associated microbes can produce gibberellin (GA) phytohormones, as first described for the rice fungal pathogen Gibberella fujikuroi and more recently for bacteria, including several rhizobia and the rice bacterial pathogen Xanthomonas oryzae pv. oryzicola. The relevant enzymes are encoded by a biosynthetic operon that exhibits both a greater phylogenetic range and scattered distribution among plant-associated bacteria. Here the phylogenetic distribution of this operon was investigated. To demonstrate conserved functionality, the enzymes encoded by the disparate operon from Xanthomonas translucens pv. translucens, along with those from the most divergent example, found in Erwinia tracheiphila, were biochemically characterized. In both of these phytopathogens the operon leads to production of the bioactive GA4. Based on these results, it seems that this operon is widely dedicated to GA biosynthesis. However, there is intriguing variation in exact product. In particular, although all plant pathogens seem to produce bioactive GA4, rhizobia generally only produce the penultimate hormonal precursor GA9. This is suggested to reflect their distinct interactions with plants, as production of GA4 counteracts the jasmonic acid-mediated defense response, reflecting the importance of wounds as the entry point for these phytopathogens, while such suppression presumably is detrimental in the rhizobial symbiotic relationship.

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Section: Discussionmentioning

confidence: 99%

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Nagel

Peters

2017

MPMI

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“…For two of them, X. albilineans and X. sacchari , genomic analyses demonstrated that they do not contain an Hrp T3SS (Pieretti et al, 2009; Studholme et al, 2011). In contrast, the 48 available genome sequences from seven different pathovars of X. translucens (Wichmann et al, 2013; Gardiner et al, 2014; Pesce et al, 2015a,b; Hersemann et al, 2016, 2017; Jaenicke et al, 2016; Peng et al, 2016) and draft genome sequence of X. hyacinthi (Naushad et al, 2015) revealed that all of them contain an Hrp T3SS the genetic organization of which is at variance to those from the clade-2.…”

Section: Introductionmentioning

confidence: 93%

Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF

et al. 2017

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Xanthomonas translucens is the causal agent of bacterial leaf streak, the most common bacterial disease of wheat and barley. To cause disease, most xanthomonads depend on a highly conserved type III secretion system, which translocates type III effectors into host plant cells. Mutagenesis of the conserved type III secretion gene hrcT confirmed that the X. translucens type III secretion system is required to cause disease on the host plant barley and to trigger a non-host hypersensitive response (HR) in pepper leaves. Type III effectors are delivered to the host cell by a surface appendage, the Hrp pilus, and a translocon protein complex that inserts into the plant cell plasma membrane. Homologs of the Xanthomonas HrpF protein, including PopF from Ralstonia solanacearum and NolX from rhizobia, are thought to act as a translocon protein. Comparative genomics revealed that X. translucens strains harbor a noncanonical hrp gene cluster, which rather shares features with type III secretion systems from Ralstonia solanacearum, Paraburkholderia andropogonis, Collimonas fungivorans, and Uliginosibacterium gangwonense than other Xanthomonas spp. Surprisingly, none of these bacteria, except R. solanacearum, encode a homolog of the HrpF translocon. Here, we aimed at identifying a candidate translocon from X. translucens. Notably, genomes from strains that lacked hrpF/popF/nolX instead encode another gene, called hpaT, adjacent to and co-regulated with the type III secretion system gene cluster. An insertional mutant in the X. translucens hpaT gene, which is the first gene of a two-gene operon, hpaT-hpaH, was non-pathogenic on barley and did not cause the HR or programmed cell death in non-host pepper similar to the hrcT mutant. The hpaT mutant phenotypes were partially complemented by either hpaT or the downstream gene, hpaH, which has been described as a facilitator of translocation in Xanthomonas oryzae. Interestingly, the hpaT mutant was also complemented by the hrpF gene from Xanthomonas euvesicatoria. These findings reveal that both HpaT and HpaH contribute to the injection of type III effectors into plant cells.

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“…CSIs and CSPs have recently been used to revise the taxonomy of a diverse range of prokaryotic groups at different taxonomic levels (e.g., Cyanobacteria, Halobacteria, Xanthomonadales and Burkholderia) Howard-Azzeh et al 2014;Sawana et al 2014;Naushad et al 2015). In this work we have identified 32 CSIs, nine of which are characteristic of the members of the phylum Chlamydiae.…”

Section: Molecular Markers Distinguishing the Two Main Groups Of Chlamentioning

confidence: 99%

A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

Gupta

Naushad

Chokshi

et al. 2015

Antonie van Leeuwenhoek

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The phylum Chlamydiae contains nine ecologically and genetically diverse families all placed within a single order. In this work, we have completed a comprehensive comparative analysis of 36 sequenced Chlamydiae genomes in order to identify shared molecular characteristics, namely conserved signature insertions/deletions (CSIs) and conserved signature proteins (CSPs), which can serve as distinguishing characteristics of supra-familial clusters within the phylum Chlamydiae. Our analysis has led to the identification of 32 CSIs which are specific to clusters within the phylum Chlamydiae at various phylogenetic depths. Importantly, 17 CSIs and 98 CSPs were found to be specific for the family Chlamydiaceae while another 3 CSI variants and 15 CSPs were specific for a grouping of the families Criblamydiaceae, Parachlamydiaceae, Simkaniaceae and Waddliaceae. These two clusters were also found to be distinguishable in 16S rRNA based phylogenetic trees, concatenated protein based phylogenetic trees, character compatibility based phylogenetic analyses, and on the basis of 16S rRNA gene sequence identity and average amino acid identity values. On the basis of the identified molecular characteristics, branching in phylogenetic trees, and the genetic distance between the two clusters within the phylum Chlamydiae we propose a division of the class Chlamydiia into two orders: an emended order Chlamydiales, containing the family Chlamydiaceae and the closely related Candidatus family Clavichlamydiaceae, and the novel order Parachlamydiales ord. nov. containing the families Parachlamydiaceae, Simkaniaceae and Waddliaceae and the Candidatus families Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae. We also include a brief discussion of the reunification of the genera Chlamydia and Chlamydophila.

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Cited by 136 publications

References 55 publications

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria

Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF

A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

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