Alphaproteobacteria Explained

Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly "Proteobacteria").[1] The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. 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.

Characteristics

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).[2] A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes.[3] 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

There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-content between members of several orders. Specifically, Pelagibacterales, Rickettsiales and Holosporales contain species with AT-rich genomes. It has been argued that it could be a case of convergent evolution that would result in an artefactual clustering.[4] [5] [6] However, several studies disagree.[7] [8] [9]

Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, even though they are more closely related to species with high genomic GC-contents than to members of the latter two orders.

The Class Alphaproteobacteria is divided into three subclasses Magnetococcidae, Rickettsidae and Caulobacteridae. The basal group is Magnetococcidae, which is composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus.[10] 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 also led to discovery of 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 novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups.[11] 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.[12] [13]

The phylogeny of Alphaproteobacteria has constantly been revisited and updated.[14] [15] There are some debates for the inclusion of Magnetococcidae in Alphaproteobacteria. For example, an independent proteobacterial class ("Candidatus Etaproteobacteria") for Magnetococcidae has been proposed.[16] [17] A recent phylogenomic study suggests the placement of the protomitochondrial clade between Magnetococcidae and all other alphaproteobacterial taxa,[18] 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

The following taxa have been assigned to the Alphaproteobacteria, but have not been assigned to one or more intervening taxonomic ranks:[19]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN). The phylogeny is based on whole-genome analysis.[23] Subclass names are based on Ferla et al. (2013).

Natural genetic transformation

Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens,[24] Methylobacterium organophilum,[25] and Bradyrhizobium japonicum.[26] 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.

External links

Notes and References

  1. Book: Bergey's Manual of Systematic Bacteriology. 2C. The Proteobacteria. Garrity GM . Brenner DJ, Krieg NR, Staley T . Springer. New York. 2nd. 978-0-387-24145-6. 1388. registration. July 26, 2005. 1984(Williams & Wilkins). British Library no. GBA561951.
  2. Martijn . Joran . Vosseberg . Julian . Guy . Lionel . Offre . Pierre . Ettema . Thijs J. G. . 2018-05-01 . Deep mitochondrial origin outside the sampled alphaproteobacteria . Nature . en . 557 . 7703 . 101–105 . 10.1038/s41586-018-0059-5 . 29695865 . 2018Natur.557..101M . 13740626 . 1476-4687. free .
  3. Chilton MD, Drummond MH, Merio DJ, Sciaky D, Montoya AL, Gordon MP, Nester EW . Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis . Cell . 11 . 2 . 263–71 . June 1977 . 890735 . 10.1016/0092-8674(77)90043-5 . 7533482 .
  4. Rodríguez-Ezpeleta N, Embley TM . The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria . PLOS ONE . 7 . 1 . e30520 . 2012 . 22291975 . 3264578 . 10.1371/journal.pone.0030520 . free . 2012PLoSO...730520R .
  5. Viklund J, Ettema TJ, Andersson SG. Siv G. E. Andersson . Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade . Molecular Biology and Evolution . 29 . 2 . 599–615 . February 2012 . 21900598 . 10.1093/molbev/msr203 .
  6. Viklund J, Martijn J, Ettema TJ, Andersson SG . Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade . PLOS ONE . 8 . 11 . e78858 . 2013 . 24223857 . 3815206 . 10.1371/journal.pone.0078858 . free . 2013PLoSO...878858V .
  7. Georgiades K, Madoui MA, Le P, Robert C, Raoult D . Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion . PLOS ONE . 6 . 9 . e24857 . 2011 . 21957463 . 3177885 . 10.1371/journal.pone.0024857 . free . 2011PLoSO...624857G .
  8. Thrash JC, Boyd A, Huggett MJ, Grote J, Carini P, Yoder RJ, Robbertse B, Spatafora JW, Rappé MS, Giovannoni SJ . 6 . Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade . Scientific Reports . 1 . 13 . 2011 . 22355532 . 3216501 . 10.1038/srep00013 . 2011NatSR...1E..13T .
  9. Williams KP, Sobral BW, Dickerman AW . A robust species tree for the alphaproteobacteria . Journal of Bacteriology . 189 . 13 . 4578–86 . July 2007 . 17483224 . 1913456 . 10.1128/JB.00269-07 .
  10. 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. 10.1099/ijs.0.038927-0 . 22581902 .
  11. Gupta RS . Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution . Critical Reviews in Microbiology . 31 . 2 . 101–35 . 2005 . 15986834 . 10.1080/10408410590922393 . 30170035 .
  12. Gupta RS . The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes . FEMS Microbiology Reviews . 24 . 4 . 367–402 . October 2000 . 10978543 . 10.1111/j.1574-6976.2000.tb00547.x . free .
  13. Gupta RS, Sneath PH . 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 . January 2007 . 17160641 . 10.1007/s00239-006-0082-2 . 32775450 . 2007JMolE..64...90G .
  14. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M . 6 . Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria' . Frontiers in Microbiology . 11 . 468 . 2020-04-07 . 32373076 . 7179689 . 10.3389/fmicb.2020.00468 . free .
  15. Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ . An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins . eLife . 8 . e42535 . February 2019 . 30789345 . 10.7554/eLife.42535 . Rokas A, Wittkopp PJ, Irisarri I . 6447387 . free .
  16. Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF . 6 . The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria . Environmental Microbiology . 19 . 3 . 1103–1119 . March 2017 . 27902881 . 10.1111/1462-2920.13637 . 32324511 .
  17. Lin W, Zhang W, Zhao X, Roberts AP, Paterson GA, Bazylinski DA, Pan Y . Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution . The ISME Journal . 12 . 6 . 1508–1519 . June 2018 . 29581530 . 5955933 . 10.1038/s41396-018-0098-9 .
  18. Martijn J, Vosseberg J, Guy L, Offre P, Ettema TJ . Deep mitochondrial origin outside the sampled alphaproteobacteria . Nature . 557 . 7703 . 101–105 . May 2018 . 29695865 . 10.1038/s41586-018-0059-5 . 2018Natur.557..101M . 13740626 . free .
  19. Web site: Euzéby JP, Parte AC . Alphaproteobacteria, not assigned to a family . June 7, 2021 . List of Prokaryotic names with Standing in Nomenclature (LPSN).
  20. Book: Advances in Microbial Physiology . 24 . . 1983 . 0-12-027724-7 . 111 . Rose AH, Tempest DW, Morris JG .
  21. https://www.uniprot.org/taxonomy/131 Tuberoidobacter
  22. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=131 Tuberoidobacter
  23. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M . 6 . Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of 'Alphaproteobacteria' . Frontiers in Microbiology . 11 . 468 . 7 April 2020 . 32373076 . 7179689 . 10.3389/fmicb.2020.00468 . free .
  24. Demanèche S, Kay E, Gourbière F, Simonet P . Natural transformation of Pseudomonas fluorescens and Agrobacterium tumefaciens in soil . Applied and Environmental Microbiology . 67 . 6 . 2617–21 . June 2001 . 11375171 . 92915 . 10.1128/AEM.67.6.2617-2621.2001 . 2001ApEnM..67.2617D .
  25. O'Connor M, Wopat A, Hanson RS . Genetic transformation in Methylobacterium organophilum . Journal of General Microbiology . 98 . 1 . 265–72 . January 1977 . 401866 . 10.1099/00221287-98-1-265 . free .
  26. Raina JL, Modi VV . Deoxyribonucleate binding and transformation in Rhizobium jpaonicum . Journal of Bacteriology . 111 . 2 . 356–60 . August 1972 . 4538250 . 251290 . 10.1128/jb.111.2.356-360.1972 .

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