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Alphaproteobacteria

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Alphaproteobacteria
Transmission electron micrograph of Wolbachia within an insect cell.
Credit:Public Library of Science / Scott O'Neill
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Garrity et al. 2006
Subclasses[1] and Orders[3]
Synonyms[3]
  • Caulobacteria Cavalier-Smith 2020
  • Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988
  • Photobacteria Gibbons and Murray 1978 (Approved Lists 1980)
  • Alphabacteria Cavalier-Smith 2002

Alphaproteobacteria or α-proteobacteria, also called α-Purple bacteria in earlier literature, is a class of bacteria in the phylum Pseudomonadota (formerly "Proteobacteria").[4] The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria.[5][6] The Alphaproteobacteria are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are gram-negative, although some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable.[4][3]

Characteristics

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The Alphaproteobacteria are a diverse taxon and comprise several phototrophic genera, several genera metabolising C1-compounds (e.g. Methylobacterium spp.), symbionts of plants (e.g. Rhizobium spp.), endosymbionts of arthropods (Wolbachia) and intracellular pathogens (e.g. Rickettsia). Moreover, the class is sister to the protomitochondrion, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells (see Endosymbiotic theory).[1][7] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[8] Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a widely distributed and may constitute over 10% of the open ocean microbial community.

Evolution and genomics

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Several points of disagreement muddy the recovery of the phylogenetic relationships among the Alphaproteobacteria clades from the genomic data. One such point centers on the placement of the Pelagibacterales stemming from the large differences in gene content (e.g. genome streamlining in Pelagibacter ubique) and GC-content between members of several orders.[1] Specifically, certain species within Pelagibacterales, Rickettsiales, and Holosporales possess AT-rich genomes, containing higher-assayed concentrations of adenine-thymine (AT) pairs than guanine-cytosine (GC) base pairs. While it could be a case of convergent evolution resulting in an artefactual clustering,[9][10][11] several studies disagree[1][12][13][14] and no consensus has been reached.

Furthermore, the GC-content of ribosomal RNA, the traditional phylogenetic marker for prokaryotes, does not correlate well with the GC-content of the genome. For example, members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.[1]

Alphaproteobacteria are divided into three subclasses, Magnetococcidae, Rickettsidae, and Caulobacteridae.[1] The basal group is Magnetococcidae, composed of a large diversity of magnetotactic bacteria only one of which, Magnetococcus marinus, is formally described.[15] The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales. The Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales, and Sneathiellales.

Comparative analyses of the sequenced genomes have revealed many conserved insertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae).

These molecular signatures provide a means to circumscribe the taxonomic groups and to identify and assign new species accurately.[16] Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.[17][18]

Other phylogenetic debates turn on the placement of Magnetococcidae and the protomitochondrion.[19][20] There are some debates for the inclusion of Magnetococcidae in Alphaproteobacteria. For example, an independent proteobacterial class ("Candidatus Etaproteobacteria") for Magnetococcidae has been proposed.[21][22] A recent phylogenomic study suggests the placement of the protomitochondrial clade between Magnetococcidae and all other alphaproteobacterial taxa,[5] which suggests an early divergence of the protomitochondrial lineage from the rest of alphaproteobacteria, except for Magnetococcidae. This phylogeny also suggests that the protomitochondrial lineage does not necessarily have a close relationship to Rickettsidae.

Incertae sedis

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The following taxa have been assigned to the Alphaproteobacteria, but have not been assigned to one or more intervening taxonomic ranks:[23]

Phylogeny

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).[3] The phylogeny is based on whole-genome analysis.[6][a] Subclass names are based on Ferla et al. (2013).[1]

Bacteria

Natural genetic transformation

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Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[28] Methylobacterium organophilum,[29] and Bradyrhizobium japonicum.[30] Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination.

Notes

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  1. ^ Holosporales and Minwuiales are omitted from this phylogenetic tree.

References

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  1. ^ a b c d e f g h i j Ferla MP, Thrash JC, Giovannoni SJ, Patrick WM (2013). "New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability". PLOS ONE. 8 (12): e83383. Bibcode:2013PLoSO...883383F. doi:10.1371/journal.pone.0083383. PMC 3859672. PMID 24349502.
  2. ^ Grote J, Thrash JC, Huggett MJ, Landry ZC, Carini P, Giovannoni SJ, Rappé MS (2012). "Streamlining and core genome conservation among highly divergent members of the SAR11 clade". mBio. 3 (5): e00252-12. doi:10.1128/mBio.00252-12. PMC 3448164. PMID 22991429.
  3. ^ a b c d Euzéby JP, Parte AC. "Alphaproteobacteria". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved May 31, 2021.
  4. ^ a b Brenner DJ, Krieg NR, Staley T (July 26, 2005) [1984(Williams & Wilkins)]. Garrity GM (ed.). The Proteobacteria. Bergey's Manual of Systematic Bacteriology. Vol. 2C (2nd ed.). New York: Springer. p. 1388. ISBN 978-0-387-24145-6. British Library no. GBA561951.
  5. ^ a b Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ (May 2018). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. Bibcode:2018Natur.557..101M. doi:10.1038/s41586-018-0059-5. PMID 29695865. S2CID 13740626.
  6. ^ a b Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (7 April 2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  7. ^ Martijn, Joran; Vosseberg, Julian; Guy, Lionel; Offre, Pierre; Ettema, Thijs J. G. (2018-05-01). "Deep mitochondrial origin outside the sampled alphaproteobacteria". Nature. 557 (7703): 101–105. Bibcode:2018Natur.557..101M. doi:10.1038/s41586-018-0059-5. ISSN 1476-4687. PMID 29695865. S2CID 13740626.
  8. ^ Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW (June 1977). "Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis". Cell. 11 (2): 263–271. doi:10.1016/0092-8674(77)90043-5. PMID 890735. S2CID 7533482.
  9. ^ Rodríguez-Ezpeleta N, Embley TM (2012). "The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria". PLOS ONE. 7 (1): e30520. Bibcode:2012PLoSO...730520R. doi:10.1371/journal.pone.0030520. PMC 3264578. PMID 22291975. Open access icon
  10. ^ Viklund J, Ettema TJ, Andersson SG (February 2012). "Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade". Molecular Biology and Evolution. 29 (2): 599–615. doi:10.1093/molbev/msr203. PMID 21900598.
  11. ^ Viklund J, Martijn J, Ettema TJ, Andersson SG (2013). "Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade". PLOS ONE. 8 (11): e78858. Bibcode:2013PLoSO...878858V. doi:10.1371/journal.pone.0078858. PMC 3815206. PMID 24223857. Open access icon
  12. ^ Georgiades K, Madoui MA, Le P, Robert C, Raoult D (2011). "Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion". PLOS ONE. 6 (9): e24857. Bibcode:2011PLoSO...624857G. doi:10.1371/journal.pone.0024857. PMC 3177885. PMID 21957463. Open access icon
  13. ^ Thrash JC, Boyd A, Huggett MJ, Grote J, Carini P, Yoder RJ, et al. (2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Scientific Reports. 1: 13. Bibcode:2011NatSR...1E..13T. doi:10.1038/srep00013. PMC 3216501. PMID 22355532.
  14. ^ Williams KP, Sobral BW, Dickerman AW (July 2007). "A robust species tree for the alphaproteobacteria". Journal of Bacteriology. 189 (13): 4578–86. doi:10.1128/JB.00269-07. PMC 1913456. PMID 17483224.
  15. ^ Bazylinski DA, Williams TJ, Lefèvre CT, Berg RJ, Zhang CL, Bowser SS, Dean AJ, Beveridge TJ (2012). "Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov.; Magnetococcales ord. nov.) at the base of the Alphaproteobacteria ". Int J Syst Evol Microbiol. 63 (Pt 3): 801–808. doi:10.1099/ijs.0.038927-0. PMID 22581902.
  16. ^ Gupta RS (2005). "Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution". Critical Reviews in Microbiology. 31 (2): 101–35. doi:10.1080/10408410590922393. PMID 15986834. S2CID 30170035.
  17. ^ Gupta RS (October 2000). "The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes". FEMS Microbiology Reviews. 24 (4): 367–402. doi:10.1111/j.1574-6976.2000.tb00547.x. PMID 10978543.
  18. ^ Gupta RS, Sneath PH (January 2007). "Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions". Journal of Molecular Evolution. 64 (1): 90–100. Bibcode:2007JMolE..64...90G. doi:10.1007/s00239-006-0082-2. PMID 17160641. S2CID 32775450.
  19. ^ Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. (2020-04-07). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria'". Frontiers in Microbiology. 11: 468. doi:10.3389/fmicb.2020.00468. PMC 7179689. PMID 32373076.
  20. ^ Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ (February 2019). Rokas A, Wittkopp PJ, Irisarri I (eds.). "An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins". eLife. 8: e42535. doi:10.7554/eLife.42535. PMC 6447387. PMID 30789345.
  21. ^ Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, et al. (March 2017). "The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria". Environmental Microbiology. 19 (3): 1103–1119. doi:10.1111/1462-2920.13637. PMID 27902881. S2CID 32324511.
  22. ^ Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y (June 2018). "Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution". The ISME Journal. 12 (6): 1508–1519. doi:10.1038/s41396-018-0098-9. PMC 5955933. PMID 29581530.
  23. ^ Euzéby JP, Parte AC. "Alphaproteobacteria, not assigned to a family". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 7, 2021.
  24. ^ Rose AH, Tempest DW, Morris JG (1983). Advances in Microbial Physiology. Vol. 24. Academic Press. p. 111. ISBN 0-12-027724-7.
  25. ^ Tuberoidobacter, on: IniProt Taxonomy
  26. ^ Tuberoidobacter, on: NCBI Taxonomy Browser
  27. ^ Roger AJ, Muñoz-Gómez SA, Kamikawa R (November 2017). "The Origin and Diversification of Mitochondria". Current Biology. 27 (21): R1177 – R1192. doi:10.1016/j.cub.2017.09.015. PMID 29112874.
  28. ^ Demanèche S, Kay E, Gourbière F, Simonet P (June 2001). "Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil". Applied and Environmental Microbiology. 67 (6): 2617–21. Bibcode:2001ApEnM..67.2617D. doi:10.1128/AEM.67.6.2617-2621.2001. PMC 92915. PMID 11375171.
  29. ^ O'Connor M, Wopat A, Hanson RS (January 1977). "Genetic transformation in Methylobacterium organophilum". Journal of General Microbiology. 98 (1): 265–72. doi:10.1099/00221287-98-1-265. PMID 401866.
  30. ^ Raina JL, Modi VV (August 1972). "Deoxyribonucleate binding and transformation in Rhizobium jpaonicum". Journal of Bacteriology. 111 (2): 356–60. doi:10.1128/jb.111.2.356-360.1972. PMC 251290. PMID 4538250.
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