Spizellomyces punctatus

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Spizellomyces punctatus
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Eukaryota
Kingdom: Fungi
Division: Chytridiomycota
Class: Chytridiomycetes
Order: Spizellomycetales
Family: Spizellomycetaceae
Genus: Spizellomyces
Species:
S. punctatus
Binomial name
Spizellomyces punctatus
(W.J. Koch) D.J.S. Barr

Spizellomyces punctatus is a chytrid fungus living in soil. [1] It is a saprotrophic fungus that colonizes decaying plant material. [2] Being an early diverging fungus, S. punctatus retains ancestral cellular features that are also found in animals and amoebae. [3] Its pathogenic relatives, Batrachochytrium dendrobatidis and B. salamandrivorans , infect amphibians and cause global biodiversity loss. [4] The pure culture of S. punctatus was first obtained by Koch (named Phlyctochytrium punctatum). [5]

Genome

The genome of S. punctatus strain DAOM BR117 was sequenced under the Origins of Multicellularity project. [6] Its genome size is about 24.13 Mb with a GC content of 47.6%. The genome has 9,424 predicted transcripts and 8,952 predicted protein-coding genes. The DDBJ/EMBL/GenBank accession number is ACOE00000000. [1]

Genetic transformation

Agrobacterium-Mediated Transformation

Genetic transformation of S. punctatus zoospores by plant pathogen Agrobacterium tumefaciens EHA105 strain is successfully established. Several selection markers have been tested. The growth of S. punctatus is not inhibited by Geneticin (G418), Puromycin, and Phleomycin D10 (Zeocin) up to 800 mg/L. 200 mg/L Hygromycin and 800 mg/L Nourseothricin (CloNAT) completely inhibit S. punctatus growth. The scientists who develop this protocol use Hygromycin as the selection marker. S. punctatus HSP70 and H2B promoters drive sufficient gene expression for Hygromycin resistance and GFP expression tested in yeast. Controlled by stronger H2B promoter, however, GFP may not be successfully folded in S. punctatus. Other fluorescent proteins, including tdTomato, mClover3, mCitrine, and mCerulean3, are functional in S. punctatus. [3]

Electroporation

A high-efficiency electroporation protocol for S.punctatus and two related chytrids species B. dendrobatidis and B. salamandrivorans has also been established. The optimal voltage for S. punctatus is 1000 V. The efficiency is about 95% using synchronized zoospores. Electroporation using unsynchronized zoospores can also reach more than 80% efficiency. [7]

Life cycle

S.punctatus globular zoospores (3–5 mm) lacks a cell wall. The zoospores can swim with a motile cilium (20–24 mm) or crawl on surfaces by actin-filled pseudopods. [3]

During encystment, the cilium is disassembled first via axoneme internalization. The initiation of this process is actin-dependent. The axoneme remains intact during internalization and the axonemal tubulin is degraded at least in part by the proteasome. The cell wall is formed after axoneme internalization. Five modes of axoneme internalization occur in S.punctatus: severing, reeling in retraction, lash-around retraction, ciliary compartment loss retraction, and vesicular retraction. First, severing is referred to as cilium detachment. Second, reeling in retraction is concurrent with or without cortical rotation and termed body-twist retraction and straight-in retraction, respectively. Third, during lash-around retraction, the cilium wraps around outside the zoospore with merging of ciliary membrane and plasma membrane. On 120 kPa fibronectin-coated hydrogels, this lash-around retraction occurs within a second. Fourth, for ciliary compartment loss retraction, ciliary membrane expansion is followed by merging of the ciliary compartment with the plasma membrane. Fifth, vesicular retraction is the creation of an axoneme loop bulge within the ciliary membrane before internalization. [8] [9]

After the cilium is retracted, the cyst germinates and generates a germ tube. The germ tube is then extended to form the rhizoidal system. Finally, the cyst develops into a sporangium, a reproductive structure, and mitosis begins. After five to eight times of synchronous mitosis, 32 – 256 zoospores form in the sporangium. Ciliogenesis probably occurs before cellularization. After cellularization, the zoospores escapes from the sporangium under suitable environmental condition. [3]

The timing of the cell cycle has been quantified using the S.punctatus expressing H2B-TdTomato controlled by H2B promoter under microscopy. The retraction of the cilium and the start of encysting happen within one hour. The germ tube appears in one to three hours. The first mitosis happens in eight to twelve hours. It finishes five to eight times of synchronous mitosis in thirty hours. The average cell cycle takes about 150 minutes. Each nuclear division is completed in 1 minute. [3]

Mitochondrial 5’ tRNA editing

This species is notable for having mitochondrial 5′ tRNA editing, a rare modification that is only known to also exist in the Amoebozoa species Acanthamoeba castellanii [1] and Chytridiomycota species Harpochytrium94, Harpochytrium105, Monoblepharella15, and Hyaloraphidium curvatum . [10] [11] S. punctatus mitochondrial genome encodes eight tRNAs that recognize lysine, aspartic acid, tryptophan, methionine, tyrosine, glutamine, proline, and leucine codons. tRNALeu recognizes the UAG codon as leucine instead of the stop codon. [10]

tRNAs form secondary structures that are composed of helical stems. Predicted from mtDNA, mismatches are found in the first three nucleotides of the eight tRNA acceptor stems. Sequencing of the mature mitochondrial tRNAs showed the replacement of pyrimidines or purines by purines (A to G, U to G, U to A, and C to A) that restore the base pairing. The editing sites are always restricted to the first three positions. [10] [12]

The mitochondrial 5’ tRNA editing of S.punctatus has been confirmed in vitro. Using mitochondrial extract, the 5’ mismatches of synthetic tRNA transcripts are removed and nucleotides are incorporated in a 3’ to 5’ direction by using the 3’ tRNA sequence as templates. The patterns of mitochondrial 5’ tRNA editing are similar to those found in A. castellanii. [13]

Phytohormone receptor homologs

Ethylene and cytokinin receptors in plants are histidine kinases. [14] Histidine kinases in fungi are hybrid histidine kinases due to the fusion of histidine kinase/histidine kinase-like ATPase catalytic domains (HK/HATPase domains) to the receiver domain. Ethylene and cytokinin receptor homologs are also found in several flagellated and unflagellated fungal genera, including Spizellomyces . In general, these two phytohormones are signaling molecules in plant biotic interactions. Ethylene and cytokinin receptors in early diversifying fungus may play important roles in colonizing land. [2]

Opsins

Two opsin types exist: [15] [16] Type 1 opsins are used by prokaryotes and by some algae (as a component of channelrhodopsins) and fungi, [17] whereas animals use type 2 opsins. [15] Type 2 opsins belong to Class A family of G-protein coupled receptors. [18] Both types are seven-transmembrane receptors and bind covalently retinal as chromophore, which turns them into photoreceptors sensing light. However, both types are not related on the sequence level. [19]

In other fungi such as Blastocladiella emersonii , a flagellated early-diverging fungus, type 1 opsins are used for phototaxis. [20] However, in S. punctatus type 1 opsins do not exist, [21] but a putative type 2 opsin. It shares with other G-protein-coupled receptors a number of conserved motifs and amino acids including the lysine corresponding to residue 296 in cattle rhodopsin, [22] which is important for retinal binding and light sensing. [23] It is as suggested by template-based structure modelling also structurally similar to animal type 2 opsins. At least computationally, it can bind retinal as chromophore. However, it prefers binding 9-cis-retinal, [22] unlike most classical animal type 2 opsins, such as cattle rhodopsin, which binds 11-cis-retinal in the dark state. [24] [25] [26] [27] [28] However, the biological function of the S. punctatus opsin is unknown. [22] Whether it is indeed a type 2 opsin is also unclear, since it is absent from a comprehensive opsin pyhlogeny that covers as many opsins as possible. [29] In principle, if it is a photoreceptor, it could have evolved light sensitivity, independently.

Fanzor endonuclease

Fanzor is a protein encoded by eukaryotic transposons and is thought to have originated from TnpB , an effector of the prokaryotic RNA-guided system known as OMEGA. TnpB is also considered the putative ancestor of Cas12, an RNA-guided endonuclease utilized in the CRISPR-Cas system. This suggests a connection between Fz, TnpB, and Cas12, despite their different roles and context in prokaryotic and eukaryotic cells. Spizellomyces punctatus was used extensively to study the structure of Fanzor. [30]

Related Research Articles

<span class="mw-page-title-main">Flagellum</span> Cellular appendage functioning as locomotive or sensory organelle

A flagellum is a hairlike 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 protists with flagella are known as flagellates.

<span class="mw-page-title-main">Cilium</span> Organelle found on eukaryotic cells

The cilium is a membrane-bound organelle found on most types of eukaryotic cell. Cilia are absent in bacteria and archaea. The cilium has the shape of a slender threadlike projection that extends from the surface of the much larger cell body. Eukaryotic flagella found on sperm cells and many protozoans have a similar structure to motile cilia that enables swimming through liquids; they are longer than cilia and have a different undulating motion.

<span class="mw-page-title-main">Chytridiomycota</span> Division of fungi

Chytridiomycota are a division of zoosporic organisms in the kingdom Fungi, informally known as chytrids. The name is derived from the Ancient Greek χυτρίδιον (khutrídion), meaning "little pot", describing the structure containing unreleased zoospores. Chytrids are one of the earliest diverging fungal lineages, and their membership in kingdom Fungi is demonstrated with chitin cell walls, a posterior whiplash flagellum, absorptive nutrition, use of glycogen as an energy storage compound, and synthesis of lysine by the α-amino adipic acid (AAA) pathway.

<span class="mw-page-title-main">Retinal</span> Chemical compound

Retinal is a polyene chromophore. Retinal, bound to proteins called opsins, is the chemical basis of visual phototransduction, the light-detection stage of visual perception (vision).

<span class="mw-page-title-main">Melanopsin</span> Mammalian protein found in Homo sapiens

Melanopsin is a type of photopigment belonging to a larger family of light-sensitive retinal proteins called opsins and encoded by the gene Opn4. In the mammalian retina, there are two additional categories of opsins, both involved in the formation of visual images: rhodopsin and photopsin in the rod and cone photoreceptor cells, respectively.

<span class="mw-page-title-main">Opsin</span> Class of light-sensitive proteins

Animal opsins are G-protein-coupled receptors and a group of proteins made light-sensitive via a chromophore, typically retinal. When bound to retinal, opsins become retinylidene proteins, but are usually still called opsins regardless. Most prominently, they are found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal, the first step in the visual transduction cascade. Another opsin found in the mammalian retina, melanopsin, is involved in circadian rhythms and pupillary reflex but not in vision. Humans have in total nine opsins. Beside vision and light perception, opsins may also sense temperature, sound, or chemicals.

<span class="mw-page-title-main">Axoneme</span> Protein structure forming the core of cilia and flagellae

In molecular biology, an axoneme, also called an axial filament, is the microtubule-based cytoskeletal structure that forms the core of a cilium or flagellum. Cilia and flagella are found on many cells, organisms, and microorganisms, to provide motility. The axoneme serves as the "skeleton" of these organelles, both giving support to the structure and, in some cases, the ability to bend. Though distinctions of function and length may be made between cilia and flagella, the internal structure of the axoneme is common to both.

<span class="mw-page-title-main">Smoothened</span> Gene found in humans and other animals

Smoothened is a protein that in humans is encoded by the SMO gene. Smoothened is a Class Frizzled G protein-coupled receptor that is a component of the hedgehog signaling pathway and is conserved from flies to humans. It is the molecular target of the natural teratogen cyclopamine. It also is the target of vismodegib, the first hedgehog pathway inhibitor to be approved by the U.S. Food and Drug Administration (FDA).

Retinylidene proteins, or rhodopsins in a broad sense, are proteins that use retinal as a chromophore for light reception. They are the molecular basis for a variety of light-sensing systems from phototaxis in flagellates to eyesight in animals. Retinylidene proteins include all forms of opsin and rhodopsin. While rhodopsin in the narrow sense refers to a dim-light visual pigment found in vertebrates, usually on rod cells, rhodopsin in the broad sense refers to any molecule consisting of an opsin and a retinal chromophore in the ground state. When activated by light, the chromophore is isomerized, at which point the molecule as a whole is no longer rhodopsin, but a related molecule such as metarhodopsin. However, it remains a retinylidene protein. The chromophore then separates from the opsin, at which point the bare opsin is a retinylidene protein. Thus, the molecule remains a retinylidene protein throughout the phototransduction cycle.

<span class="mw-page-title-main">Rhizophydiales</span> Order of fungi

Rhizophydiales are an important group of chytrid fungi. They are found in soil as well as marine and fresh water habitats where they function as parasites and decomposers.

<span class="mw-page-title-main">RRH</span> Protein-coding gene in the species Homo sapiens

Peropsin, a visual pigment-like receptor, is a protein that in humans is encoded by the RRH gene. It belongs like other animal opsins to the G protein-coupled receptors. Even so, the first peropsins were already discovered in mice and humans in 1997, not much is known about them.

<span class="mw-page-title-main">OPN5</span> Protein-coding gene in the species Homo sapiens

Opsin-5, also known as G-protein coupled receptor 136 or neuropsin is a protein that in humans is encoded by the OPN5 gene. Opsin-5 is a member of the opsin subfamily of the G protein-coupled receptors. It is a photoreceptor protein sensitive to ultraviolet (UV) light. The OPN5 gene was discovered in mouse and human genomes and its mRNA expression was also found in neural tissues. Neuropsin is bistable at 0 °C and activates a UV-sensitive, heterotrimeric G protein Gi-mediated pathway in mammalian and avian tissues.

<span class="mw-page-title-main">Retinal G protein coupled receptor</span> Protein-coding gene in the species Homo sapiens

RPE-retinal G protein-coupled receptor also known as RGR-opsin is a protein that in humans is encoded by the RGR gene. RGR-opsin is a member of the rhodopsin-like receptor subfamily of GPCR. Like other opsins which bind retinaldehyde, it contains a conserved lysine residue in the seventh transmembrane domain. RGR-opsin comes in different isoforms produced by alternative splicing.

<span class="mw-page-title-main">Retinitis pigmentosa GTPase regulator</span> Protein-coding gene in the species Homo sapiens

X-linked retinitis pigmentosa GTPase regulator is a GTPase-binding protein that in humans is encoded by the RPGR gene. The gene is located on the X-chromosome and is commonly associated with X-linked retinitis pigmentosa (XLRP). In photoreceptor cells, RPGR is localized in the connecting cilium which connects the protein-synthesizing inner segment to the photosensitive outer segment and is involved in the modulation of cargo trafficked between the two segments.

<span class="mw-page-title-main">ARR3</span> Protein-coding gene in humans

Arrestin-C, also known as retinal cone arrestin-3, is a protein that in humans is encoded by the ARR3 gene.

<span class="mw-page-title-main">MORM syndrome</span> Medical condition

MORM syndrome is an autosomal recessive congenital disorder characterized by mental retardation, truncal obesity, retinal dystrophy, and micropenis". The disorder shares similar characteristics with Bardet–Biedl syndrome and Cohen syndrome, both of which are autosomal recessive genetic disorders. MORM syndrome can be distinguished from the above disorders because symptoms appear at a young age. The disorder is not dependent on sex of the offspring, both male and female offspring are equally likely to inherit the disorder.

<span class="mw-page-title-main">Phototaxis</span>

Phototaxis is a kind of taxis, or locomotory movement, that occurs when a whole organism moves towards or away from a stimulus of light. This is advantageous for phototrophic organisms as they can orient themselves most efficiently to receive light for photosynthesis. Phototaxis is called positive if the movement is in the direction of increasing light intensity and negative if the direction is opposite.

<span class="mw-page-title-main">Retinal degeneration (rhodopsin mutation)</span> Retinopathy

Retinal degeneration is a retinopathy which consists in the deterioration of the retina caused by the progressive death of its cells. There are several reasons for retinal degeneration, including artery or vein occlusion, diabetic retinopathy, R.L.F./R.O.P., or disease. These may present in many different ways such as impaired vision, night blindness, retinal detachment, light sensitivity, tunnel vision, and loss of peripheral vision to total loss of vision. Of the retinal degenerative diseases retinitis pigmentosa (RP) is a very important example.

Ciliogenesis is defined as the building of the cell's antenna or extracellular fluid mediation mechanism. It includes the assembly and disassembly of the cilia during the cell cycle. Cilia are important organelles of cells and are involved in numerous activities such as cell signaling, processing developmental signals, and directing the flow of fluids such as mucus over and around cells. Due to the importance of these cell processes, defects in ciliogenesis can lead to numerous human diseases related to non-functioning cilia. Ciliogenesis may also play a role in the development of left/right handedness in humans.

<span class="mw-page-title-main">Vertebrate visual opsin</span>

Vertebrate visual opsins are a subclass of ciliary opsins and mediate vision in vertebrates. They include the opsins in human rod and cone cells. They are often abbreviated to opsin, as they were the first opsins discovered and are still the most widely studied opsins.

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