Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

Gupta, Radhey S.; Lorenzini, Emily

doi:10.1186/1471-2148-7-71

Cited by 67 publications

(55 citation statements)

References 74 publications

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“…It is well known that Bacteroidetes's closest living relatives are the Chlorobi (Gupta and Lorenzini 2007), so this HGT event suggests that the divergence of Bacteroidetes and the Chlorobi occurred after the evolution of eukaryotes. This is consistent with biomarker evidence for the origin of the phylum Chlorobi in the geochemical record 1.6 billion years ago (Brocks et al 2005), which is coincidental with red algae fossils (Bengtson et al 2017) and other well-documented fossils of early eukaryotes (Butterfield 2015).…”

Section: Discussionmentioning

confidence: 99%

Early emergence of the FtsH proteases involved in photosystem II repair

Shao¹,

Cardona²,

Nixon³

2018

Photosynt.

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Efficient degradation of damaged D1 during the repair of PSII is carried out by a set of dedicated FtsH proteases in the thylakoid membrane. Here we investigated whether the evolution of FtsH could hold clues to the origin of oxygenic photosynthesis. A phylogenetic analysis of over 6000 FtsH protease sequences revealed that there are three major groups of FtsH proteases originating from gene duplication events in the last common ancestor of bacteria, and that the FtsH proteases involved in PSII repair form a distinct clade branching out before the divergence of FtsH proteases found in all groups of anoxygenic phototrophic bacteria. Furthermore, we showed that the phylogenetic tree of FtsH proteases in phototrophic bacteria is similar to that for Type I and Type II reaction centre proteins. We conclude that the phylogeny of FtsH proteases is consistent with an early origin of photosynthetic water oxidation chemistry.

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Section: Discussionmentioning

confidence: 99%

Early emergence of the FtsH proteases involved in photosystem II repair

Shao¹,

Cardona²,

Nixon³

2018

Photosynt.

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“…These bacteria are present in various terrestrial and marine environments. The Bacteroidetes exhibit various phenotypes including gliding behavior and their ability to digest a variety of complex substrates such as cellulose, chitin, and agar (Gupta and Lorenzini 2007). They inhabit many habitats including the oral cavity of humans, the mammalian gastrointestinal tract, marine and fresh water, and soil.…”

Section: Discussionmentioning

confidence: 99%

Seasonal variations in airborne bacterial community structures at a suburban site of central Japan over a 1-year time period using PCR-DGGE method

et al. 2014

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Airborne bacteria could affect human health and climate. In this study, the bacterial community structures were investigated by analyzing air samples collected from a suburban location in Toyama, central Japan. Sixty samples were collected almost weekly between March 2009 and February 2010. A cultivation-independent approach, PCR plus denaturing gradient gel electrophoresis (DGGE), was used to analyze changes in the structure of the airborne bacterial communities. The DGGE profiles showed significant differences between sampling days, reflecting quite different bacterial profiles. Sequencing of DGGE bands revealed that the bacterial community was dominated by c-Proteobacteria, Firmicutes, aProteobacteria, Bacteroidetes, and Actinobacteria. The most frequently observed genus was Pseudomonas, followed by Bacillus. The airborne bacterial assemblage in winter differed from that in the other seasons. The differences could be attributed a number of factors, such as temperature, relative humidity, wind direction, and snowfall. In spring, the largest number of bands was classified as plant chloroplasts, such as Japanese cedar (Cryptomeria japonica) and Pinus spp., which are the major pollen allergen sources in Japan. The airborne bacterial abundance estimated by real-time TaqMan PCR ranged from 1.1 9 10 3 to 1.3 9 10 5 cells m -3 .

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“…(Kainth and Gupta 2005;Gao et al 2009;Gupta 2006Gupta , 2009Griffiths and Gupta 2007;Gupta and Lorenzini 2007;Gupta and Mok 2007;Gupta and Shami 2011). The identified CSPs unique to different prokaryotic groups have proved of great value in defining these major groups and have also provided useful information regarding the branching order of different lineages within them.…”

Section: Conserved Indels and Lineage-specific Proteins As Novel Toolmentioning

confidence: 96%

Microbial systematics in the post-genomics era

Gao

Gupta

2011

Antonie van Leeuwenhoek

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Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved. Some of these include: how to define and delimit a prokaryotic species; development of rationale criteria for the assignment of higher taxonomic ranks; understanding what unique properties distinguish species from different groups; and understanding the branching order and interrelationship among higher prokaryotic clades. The sequencing of genomes from large numbers of cultured as well as uncultured microbes covering prokaryotic diversity provides unique means to achieve these important objectives. Prokaryotic genomes are found to be very diverse and dynamic and horizontal gene transfers (HGTs) are indicated to have played important role in species/genome evolution. Although HGT adds a layer of complexity in terms of understanding the genomes and species evolution, it is contended that vast majority of genes and genetic characteristics that are distinctive characteristics of higher prokaryotic taxa are vertically inherited and based on them a solid foundation for microbial systematics can be developed. We describe two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships. The genetic and biochemical studies on these taxa-specific molecular markers also open the way to discover novel biochemical and physiological characteristics that are unique properties of these groups.

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Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

Cited by 67 publications

References 74 publications

Early emergence of the FtsH proteases involved in photosystem II repair

Early emergence of the FtsH proteases involved in photosystem II repair

Seasonal variations in airborne bacterial community structures at a suburban site of central Japan over a 1-year time period using PCR-DGGE method

Microbial systematics in the post-genomics era

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