Jakobid

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Jakobid
Jakobida.svg
Four jakobid species, showing groove and flagella: Jakoba libera (ventral view), Stygiella incarcerata (ventral view), Reclinomonas americana (dorsal view), and Histiona aroides (ventral view)
Scientific classification
Domain:
Class:
Jakobea
Order:
Jakobida
Families

Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup of Excavates. They are small (less than 15 μm), and can be found in aerobic and anaerobic environments.[1][2][3] The order Jakobida, believed to be monophyletic, consists of only twenty species at present, and was classified as a group in 1993.[1][3][4] There is ongoing research into the mitochondrial genomes of jakobids, which are unusually large and bacteria-like, evidence that jakobids may be important to the evolutionary history of eukaryotes.[2][5]

Molecular phylogenetic evidence suggests strongly that jakobids are most closely related to Heterolobosea (Percolozoa) and Euglenozoa.[6]

Structure and Biology[edit]

Jakobids have two flagella, inserted in the anterior end of the cell, and, like other members of order Excavata, have a ventral feeding groove and associated cytoskeleton support[7]. The posterior flagella has a dorsal vane and is aligned within the ventral groove, where it generates a current that the cell uses for food intake.[5] [7] The nucleus is generally in the anterior part of the cell and bears a nucleolus. Most known jakobids have one mitochondrion, again located anteriorly, and different genera have flattened, tubular, or absent cristae. Food vacuoles are mostly located on the cell posterior, and in most jakobids the endoplasmic reticulum is distributed throughout the cell.[4]

The sessile, loricate Histionidae and occasionally free-swimming Jakoba libera (Jakobidae) have extrusomes under the dorsal membrane that are theorized to be defensive structures.[1][4]

Ecology[edit]

Jakobids are widely dispersed, having been found in soil, freshwater, and marine habitats, but generally not common.[2][5][4][8] However, environmental DNA surveys suggest that Stygiellidae are abundant in anoxic marine habitats.[4][9] Some are capable of surviving hypersaline and anoxic environments, though the Histionids have only been found in freshwater ecosystems, where they attach themselves to algae or zooplankton.[4] Outside of obligate sessile species, many species of jakobids can attach temporarily to surfaces, using either of the two flagella or the cell body itself.[9]

All known jakobids are heterotrophic suspension feeders.[2][4] Their primary prey is generally considered to be bacteria, though one species has been observed eating extremely small (< 1 µm) eukaryotic cells.[3][10] Jakobids are generally slow swimmers, with low clearance rates relative to similar organisms.[4]

No study has suggested jakobids might be pathogenic or toxic.[4]

Mitchondrial DNA[edit]

Since jakobids have no current commercial use, most research into jakobids has focused on their evolutionary significance. The mitochondrial DNA of jakobids is the most bacteria-like of all known eukaryotic mitochondrial DNA, suggesting that jakobid mitochondrial genomes might approximate the ancestral mitochondrial genome.[4]

Jakobid mitochondrial DNA is substantially different from most other eukaryotes, especially in terms of the number of genes (nearly 100 in some species) and bacteria-like elements within their genomes.[3][4] Nine of the genes have never been found in eukaryotic mitochondrial DNA. Uniquely, jakobid mitochondrial genomes code for bacteria-type RNA polymerase, as opposed to typical eukaryotic mitochondrial RNA polymerase, referred to as “phage-type”, which appears to be viral in origin.[4] This does not necessarily mean that jakobids are basal to the phylogeny of eukaryotes. While jakobid mitochondria have genetic features that seem to have developed from bacteria, and apparently lack phage-type RNA, it is possible that other eukaryotic clades lost their bacterial features independently.[11]

Several proposed possibilities might explain the bacterial features of jakobid mitochondrial DNA. One is that jakobids diverged very early from the rest of the eukaryotes. This hypothesis depends on whether or not jakobids are indeed basal to all living eukaryotes, but there is no evidence yet to support that suggestion.[4]

Another hypothesis is that the phage-type RNA polymerase moved from one eukaryote group to another via lateral gene transfer, replacing the bacteria-type enzyme, and simply did not reach the jakobids. This would not depend on jakobids being basal to eukaryotes as a whole, but has not been widely studied.[4]

A third possibility is the reverse of the others, suggesting that the phage-type RNA polymerase is the basal one. Under this scenario, jakobids acquired their bacteria-type RNA polymerase much more recently and that then spread via lateral gene transfer.[4] However, the gene arrangement of jakobid mitochondrial DNA suggests an ancestral origin of bacteria-type RNA polymerase over a more-recent divergence.[3][4]

The last of the proposed scenarios suggests that the common ancestor of eukaryotes had two mitochondrial RNA polymerases, both phage-type and bacteria-type, and jakobids lost their phage-type polymerase while the rest of the eukaryotes lost the bacteria-type, possibly several times.[4][12] Such a model eliminates the need for jakobids to be truly basal. One study proposed that the phage-type and bacteria-type polymerases, when present in the same mitochondrion, served different functions, much in the way that the organelles of land plants have two different RNA polymerase enzymes that transcribe different genes.[4]

Taxonomy[edit]

Jakobida contains five families consisting of mostly free-swimming genera: Jakobidae, Moramonadidae, Andaluciidae, and Stygiellidae.[4] The sixth family, Histionidae, is largely populated by sessile loricate genera, and includes the first jakobids ever described.[4]

Jakobids are a monophyletic group, and are most closely related to the Euglenozoa and Heterolobosea.[3][4][11]

See also[edit]

References[edit]

  1. ^ a b c O'Kelly, Charles J. (1993). "The Jakobid flagellates: structural features of Jakoba, Reclinomonas, and Histonia and implications for the early diversification of eukaryotes". Journal of Eukaryotic Microbiology. 40 (5): 627–636.
  2. ^ a b c d Strassert, Jürgen F. H.; Tikhonenov, Denis V.; Pombert, Jean-François; Kolisko, Martin; Tai, Vera; Mylnikov, Alexander P.; Keeling, Patrick J. (2016). "Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome". Open Biology. 6 (2): 150239. doi:10.1098/rsob.150239. PMC 4772810. PMID 26887409.
  3. ^ a b c d e f Burger, Gertraud; Gray, Michael W.; Forget, Lise; Lang, B. Franz (2013). "Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists". Genome Biology and Evolution. 5 (2): 418–438.
  4. ^ a b c d e f g h i j k l m n o p q r s t u Simpson, Alastair G. B. (2017). "Jakobids". In Archibald, John M.; Simpson, Alastair G. B.; Slamovits, Claudio H. Handbook of the Protists. Springer, Cham. pp. 973–1003. doi:10.1007/978-3-319-28149-0_6. ISBN 978-3-319-28147-6.
  5. ^ a b c Lara, Enrique; Chatzinotas, Antonis; Simpson, Alastair G. B. (2006). "Andalucia (n. gen.)—the Deepest Branch Within Jakobids (Jakobida; Excavata), Based on Morphological and Molecular Study of a New Flagellate from Soil". Journal of Eukaryotic Microbiology. 53 (2): 112–120. doi:10.1111/j.1550-7408.2005.00081.x. PMID 16579813.
  6. ^ Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ (February 2009). "Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"". Proc. Natl. Acad. Sci. U.S.A. 106 (10): 3859–64. Bibcode:2009PNAS..106.3859H. doi:10.1073/pnas.0807880106. PMC 2656170. PMID 19237557.
  7. ^ a b Simpson, Alastair G. B.; Patterson, David J. (2001). "On Core Jakobids and Excavate Taxa: The Ultrastructure of Jakoba incarcerata". Journal of Eukaryotic Microbiology. 48 (4): 480–492. doi:10.1111/j.1550-7408.2001.tb00183.x.
  8. ^ Lara, Enrique; Berney, Cedric; Ekelund, Flemming; Harms, Hauke; Chatzinotas, Antonis (2007). "Molecular comparison of cultivable protozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site". Soil Biology and Biochemistry. 39 (1): 139–148.
  9. ^ a b c Pánek, Tomáš; Táborský, Petr; Pachiadaki, Maria G.; Hroudová, Miluše; Vlček, Čestmir; Edgcomb, Virginia P.; Čepička, Ivan (2015). "Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage". Frontiers in Microbiology. 6: art. 1288. doi:10.3389/fmicb.2015.01288. PMC 4649034. PMID 26635756.
  10. ^ Christaki, Urania; Vázquez-Domínguez, Evaristo; Courties, Claude; Lebaron, Phillipe (2005). "Grazing impact of different heterotrophic nanoflagellates on eukaryotic (Ostreococcus tauri) and prokaryotic picoautotrophs (Prochlorococcus and Synechococcus)". Environmental Microbiology. 7 (8): 1200–1210. doi:10.1111/j.1462-2920.2005.00800.x. PMID 16011757.
  11. ^ a b Rodriguez-Ezpeleta, Naiara; Brinkmann, Henner; Burger, Gertraud; Roger, Andrew J.; Gray, Michael W.; Philippe, Herve; Lang, B. Franz (2007). "Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans". Current Biology. 17 (16): 1420–1425.
  12. ^ Stechmann, Alexandra; Cavalier-Smith, Thomas (2002). "Rooting the Eukaryote Tree by Using a Derived Gene Fusion". Science. 297 (5578): 89–91. doi:10.1126/science.1071196. PMID 12098695.