Jakoba Bahamensis
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''Jakoba'' is a genus in the taxon
Excavata Excavata is an obsolete, extensive and diverse paraphyletic group of unicellular Eukaryota. The group was first suggested by Simpson and Patterson in 1999 and the name latinized and assigned a rank by Thomas Cavalier-Smith in 2002. It contains ...
, and currently has a single described species, ''
Jakoba libera ''Jakoba'' is a genus in the taxon Excavata, and currently has a single described species, '' Jakoba libera'' described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (Previously d ...
'' described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (Previously described ''Jakoba incarcerata'' has been renamed '' Andalucia incarcerata'', and '' Jakoba bahamensis'' /''
Jakoba bahamiensis ''Jakoba'' is a genus in the taxon Excavata, and currently has a single described species, ''Jakoba libera'' described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (Previously de ...
'' is not formally described.)


Appearance and characteristics

''Jakoba'' are small bacterivorous zooflagellates (
jakobid Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. They are small (less than 15  μm), and can be found in aerobic and anaerobic environments. The order Jakobida, b ...
s) found in marine and
hypersaline A hypersaline lake is a landlocked body of water that contains significant concentrations of sodium chloride, brines, and other salts, with saline levels surpassing those of ocean water (3.5%, i.e. ). Specific microbial species can thrive i ...
environments. They are free swimming trophic cells with two
flagella A flagellum (; : flagella) (Latin for 'whip' or 'scourge') is a hair-like appendage that protrudes from certain plant and animal sperm cells, from fungal spores ( zoospores), and from a wide range of microorganisms to provide motility. Many pr ...
and range between five and ten micrometers in length. Cells rotate along their longitudinal axis to allow for swimming in straight lines unless deformation and “squirming” occurs due to compression in debris. During feeding, bacteria are removed from the water column by a current created by the posterior
flagellum A flagellum (; : flagella) (Latin for 'whip' or 'scourge') is a hair-like appendage that protrudes from certain plant and animal sperm cells, from fungal spores ( zoospores), and from a wide range of microorganisms to provide motility. Many pr ...
. This current causes the bacteria to collect in the groove on the right ventral side of the cell – aiding in ingestion and the creation of food
vacuoles A vacuole () is a membrane-bound organelle which is present in plant and fungal cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic mo ...
.


Ultrastructure

Cellular components for ''Jakoba'' are not particularly unique. They contain a single
nucleus Nucleus (: nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucleu ...
found close to the flagellar bases, a single
Golgi body The Golgi apparatus (), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles in ...
, and the
mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
cristae A crista (; : cristae) is a fold in the inner membrane of a mitochondrion. The name is from the Latin for ''crest'' or ''plume'', and it gives the inner membrane its characteristic wrinkled shape, providing a large amount of surface area for che ...
are flattened suggesting a relationship with other platicristate taxa. The
mitochondria A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...
of ''Jakoba'' are of particular interest evolutionarily due to their unique
bacterial Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the ...
-like
mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
s. It has been found that their
mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
s contain considerably more functional
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s than those of other
eukaryotic The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...
groups and it appears they have retained the ancestral eubacterial
RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template. Using the e ...
, which has been replaced by viral type polymerase in all other mitochondriate eukaryotes. Overall,
jakobid Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. They are small (less than 15  μm), and can be found in aerobic and anaerobic environments. The order Jakobida, b ...
mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
genomes A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
are primitively complex in that they resemble their proteobacterial ancestors more than any other
mitochondria A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is us ...
.


Life cycle

''Jakoba'' reproduce asexually by
binary fission Binary may refer to: Science and technology Mathematics * Binary number, a representation of numbers using only two values (0 and 1) for each digit * Binary function, a function that takes two arguments * Binary operation, a mathematical o ...
. The sexual reproduction or the formation of
cysts A cyst is a closed Wikt:sac, sac, having a distinct Cell envelope, envelope and cell division, division compared with the nearby Biological tissue, tissue. Hence, it is a cluster of Cell (biology), cells that have grouped together to form a sac ...
have not been observed.


Molecular sequence data

“The circular mitochondrial genome of ''Jakoba libera'' strain ATCC 50422 is 96.6 kbp in size. Sequencing is nearly completed. At present, 77 genes have been identified, none of them including an intron. Intergenic regions account for ~ 30% of the genome and contain clusters of tandem repeats whose unit length is ~20 bp. Transcribed genes are found on both DNA strands. The standard
genetic code Genetic code is a set of rules used by living cell (biology), cells to Translation (biology), translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets or codons) into proteins. Translation is accomplished ...
is used for
translation Translation is the communication of the semantics, meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The English la ...
. Encoded genes include those commonly found in
mtDNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in ...
, including the protein-coding genes nad1,2,3,4,4L,5,6, cob, cox1,2,3, and atp6,8,9, as well as large subunit (rnl) and small subunit (rns) rRNA genes and >22
tRNA Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...
genes. Also present are a number of protein genes typical of protist but not animal or fungal mtDNAs. These include nad7,9,11, atp1, rpl2,5,6,14,16, and rps2-4,11-14,19. A number of unique ORFs are also encoded by ''J. libera''
mtDNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in ...
.” “A number of ''J. libera'' mitochondrial genes are rare or absent in other mitochondrial genomes but are present in
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. Among these rare or unique
mtDNA Mitochondrial DNA (mtDNA and mDNA) is the DNA located in the mitochondria organelles in a eukaryotic cell that converts chemical energy from food into adenosine triphosphate (ATP). Mitochondrial DNA is a small portion of the DNA contained in ...
-encoded genes are dpo, rpoB,C, rrn5, rnpB, tufA, yejU-W, and several of the ribosomal protein genes.” “A comparison of gene order in the mtDNAs of ''J. libera''…” show “clusters that are otherwise not found in
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
but that evidently appeared during evolution of the mitochondrial genome after the divergence of the proto-mitochondrion from the bacterial lineage. Examples are the clusters sdh3 to nad5, (comprising 5 genes), atp8- rnrps4-atp9 and nad11-nad1-cox11-cox3-tufA.”


Cultures

There are currently three strains of ''Jakoba libera'' available for culture. They can not be grown axenically, but are easily raised in minimal media with added bacteria (''
Klebsiella aerogenes ''Klebsiella aerogenes'', previously known as ''Enterobacter aerogenes'', is a Gram-negative, oxidase-negative, catalase-positive, citrate-positive, indole-negative, rod-shaped bacterium. Capable of motility via peritrichous flagella, it is appr ...
'')


Similar genera

Jakobids Jakobida is an order (biology), order (sole order in the Class (biology), class Jakobea) of free-living, Heterotroph, heterotrophic, Flagellate, flagellar eukaryotes in the clade Excavata#Discoba or JEH clade, Discoba. They are small (less than 15& ...
('' Jakobida'' or ''
Jakobea Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. They are small (less than 15  μm), and can be found in aerobic and anaerobic environments. The order Jakobida, ...
'') * ''
Histiona ''Histiona'' is a genus of Excavata containing four species. It has a worldwide distribution. It is a Jakobid Jakobida is an order (sole order in the class Jakobea) of free-living, heterotrophic, flagellar eukaryotes in the clade Discoba. The ...
'': 2-3 species * ''
Reclinomonas ''Reclinomonas'' is a monotypic genus of jakobid eukaryotes containing the single species ''Reclinomonas americana''.Simpson, A. 2008''Reclinomonas'' Flavin & Nerad 1993. ''Reclinomonas americana'' Flavin & Nerad 1993.Version 05. The Tree of Life ...
'': 1 species ''
Malawimonas ''Malawimonas'' is genus of unicellular, heterotrophic flagellates with uncertain phylogenetic affinities. They have variably being assigned to Excavata and Loukozoa. Recent studies suggest they may be closely related to the Podiata. Discovery ...
'': 1 described species Retortamonads: * ''
Retortamonas ''Retortamonas'' is a genus of flagellated excavates. It is one of only two genera belonging to the family Retortamonadidae along with the genus ''Chilomastix''. Martinez-Diaz, R. A., Castro, A. T., Herrera, S. and Ponce, F. 2001: First Repo ...
'' * ''
Chilomastix ''Chilomastix'' is a genus of pyriform excavates within the family Retortamonadidae. All species within this genus are flagellated, structured with three flagella pointing anteriorly and a fourth contained within the feeding groove. ''Chilomas ...
'' Carpediemonas-like organisms: * '' Carpediemonas'' * '' Dysnectes'' * '' Hicanonectes'' * '' Ergobibamus'' * '' Kipferlia''


References

{{Taxonbar, from=Q6125390 Discoba genera Jakobids