Editing Diatom (section)

==Silicification==
{{see also|Silicification}}

Diatom cells are contained within a unique silica [[cell wall]] known as a [[frustule]] made up of two valves called [[theca]]e, that typically overlap one another.<ref>{{cite web|title=Diatoms|url=http://www.ucl.ac.uk/GeolSci/micropal/diatom.html|access-date=13 February 2016|archive-date=2 February 2016|archive-url=https://web.archive.org/web/20160202141717/http://www.ucl.ac.uk/GeolSci/micropal/diatom.html|url-status=live}}</ref> The [[biogenic silica]] composing the cell wall is [[biosynthesis|synthesised]] [[intracellular]]ly by the [[polymerisation]] of [[silicic acid]] [[monomer]]s. This material is then extruded to the cell exterior and added to the wall. In most species, when a diatom divides to produce two daughter cells, each cell keeps one of the two-halves and grows a smaller half within it. As a result, after each division cycle, the average size of diatom cells in the population gets smaller. Once such cells reach a certain minimum size, rather than simply divide, they reverse this decline by forming an [[auxospore]], usually through [[meiosis]] and sexual reproduction, but exceptions exist. The auxospore expands in size to give rise to a much larger cell, which then returns to size-diminishing divisions.<ref>[https://books.google.com/books?id=xyFvEAAAQBAJ&dq=diatoms+sexual+reproduction+auxospore+frustule&pg=PA295 The Molecular Life of Diatoms]</ref>

[[File:Pennate diatom infected with two chytrid-like fungal pathogens.png|thumb|upright=1.4| [[Pennate diatom]] from an Arctic [[meltpond]], infected with two [[Chytridiomycota|chytrid-like]] [zoo-]sporangium fungal pathogens (in false-colour red). Scale bar = 10 μm.<ref>{{cite journal |doi=10.1038/s42003-020-0891-7 |title=Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean |year=2020 |last1=Kilias |first1=Estelle S. |last2=Junges |first2=Leandro |last3=Šupraha |first3=Luka |last4=Leonard |first4=Guy |last5=Metfies |first5=Katja |last6=Richards |first6=Thomas A. |journal=Communications Biology |volume=3 |issue=1 |page=183 |pmid=32317738 |pmc=7174370 |s2cid=216033140}}</ref>]]
[[File:20110123 185042 Diatom.jpg|thumb|upright=1.4| Light microscopy of a living diatom. Numbered graduations are 10 micrometres apart]]

The exact mechanism of transferring [[silica]] absorbed by the diatom to the [[cell wall]] is unknown. Much of the sequencing of diatom genes comes from the search for the mechanism of silica uptake and deposition in nano-scale patterns in the [[frustule]]. The most success in this area has come from two species, ''[[Thalassiosira pseudonana]]'', which has become the model species, as the whole genome was sequenced and methods for genetic control were established, and ''Cylindrotheca fusiformis'', in which the important silica deposition proteins silaffins were first discovered.<ref name="hildebrand06">{{cite journal|last1=Thamatrakoln|first1=K.|title=Comparative Sequence Analysis of Diatom Silicon Transporters: Toward a Mechanistic Model of Silicon Transport|last2=Alverson|first2=A. J.|last3=Hildebrand|first3=M.|journal=Journal of Phycology|date=2006|volume=42|issue=4|pages=822–834|doi=10.1111/j.1529-8817.2006.00233.x|bibcode=2006JPcgy..42..822T |s2cid=86674657}}</ref> Silaffins, sets of polycationic [[peptides]], were found in ''C. fusiformis'' cell walls and can generate intricate silica structures. These structures demonstrated pores of sizes characteristic to diatom patterns. When ''T. pseudonana'' underwent genome analysis it was found that it encoded a [[urea cycle]], including a higher number of [[polyamines]] than most genomes, as well as three distinct silica transport genes.<ref>{{cite journal|last1=Kröger|first1=Nils|last2=Deutzmann|first2=Rainer|last3=Manfred|first3=Sumper|s2cid=10925689|title=Polycationic Peptides from Diatom Biosilica That Direct Silica Nanosphere Formation.|journal=Science|date=November 1999|volume=286|issue=5442|pages=1129–1132|doi=10.1126/science.286.5442.1129|pmid=10550045}}{{Dead link|date=March 2020 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> In a [[phylogenetic]] study on silica transport genes from 8 diverse groups of diatoms, silica transport was found to generally group with species.<ref name="hildebrand06" /> This study also found structural differences between the silica transporters of pennate (bilateral symmetry) and centric (radial symmetry) diatoms. The sequences compared in this study were used to create a diverse background in order to identify residues that differentiate function in the silica deposition process. Additionally, the same study found that a number of the regions were conserved within species, likely the base structure of silica transport.

These silica transport proteins are unique to diatoms, with no [[homologs]] found in other species, such as sponges or rice. The divergence of these silica transport genes is also indicative of the structure of the protein evolving from two repeated units composed of five membrane bound segments, which indicates either gene duplication or [[Protein dimer|dimerization]].<ref name="hildebrand06" /> The silica deposition that takes place from the membrane bound vesicle in diatoms has been hypothesized to be a result of the activity of silaffins and long chain polyamines. This Silica Deposition Vesicle (SDV) has been characterized as an acidic compartment fused with Golgi-derived vesicles.<ref>{{cite book|last1=Kroger|first1=Nils|title=Handbook of Biomineralization: Biological Aspects and Structure Formation|date=2007|publisher=Wiley-VCH Verlag GmbH|location=Weinheim, Germany|pages=chapter 3}}</ref> These two protein structures have been shown to create sheets of patterned silica [[in-vivo]] with irregular pores on the scale of diatom [[frustules]]. One hypothesis as to how these proteins work to create complex structure is that residues are conserved within the SDV's, which is unfortunately difficult to identify or observe due to the limited number of diverse sequences available. Though the exact mechanism of the highly uniform deposition of silica is as yet unknown, the ''Thalassiosira pseudonana'' genes linked to silaffins are being looked to as targets for genetic control of nanoscale silica deposition.

The ability of diatoms to make [[silica|silica-based]] [[cell wall]]s has been the subject of fascination for centuries. It started with a microscopic observation by an anonymous English country nobleman in 1703, who observed an object that looked like a chain of regular parallelograms and debated whether it was just crystals of salt, or a plant.<ref>Anonymous (1702). "Two letters from a Gentleman in the Country, relating to Mr. Leeuwenhoek's Letter in Transaction, no. 283.", ''Philos. Trans. R. Soc. Lond. B'', '''23''': 1494–1501.</ref> The viewer decided that it was a plant because the parallelograms didn't separate upon agitation, nor did they vary in appearance when dried or subjected to warm water (in an attempt to dissolve the "salt"). Unknowingly, the viewer's confusion captured the essence of diatoms—mineral utilizing plants. It is not clear when it was determined that diatom cell walls are made of silica, but in 1939 a seminal reference characterized the material as [[silicic acid]] in a "subcolloidal" state<ref>Rogall, E. (1939). "[https://www.jstor.org/stable/23357402 Ueber den feinbau der kieselmembran der diatomeen"], ''Planta'': 279-291.</ref> Identification of the main chemical component of the cell wall spurred investigations into how it was made. These investigations have involved, and been propelled by, diverse approaches including, microscopy, chemistry, biochemistry, [[material characterisation]], [[molecular biology]], [['omics]], and [[transgenic]] approaches. The results from this work have given a better understanding of cell wall formation processes, establishing fundamental knowledge which can be used to create models that contextualise current findings and clarify how the process works.<ref name=Hildebrand2018>{{cite journal | last1=Hildebrand | first1=Mark | last2=Lerch | first2=Sarah J. L. | last3=Shrestha | first3=Roshan P. | title=Understanding Diatom Cell Wall Silicification—Moving Forward | journal=Frontiers in Marine Science | publisher=Frontiers Media SA | volume=5 | date=2018-04-11 | page=125 | issn=2296-7745 | doi=10.3389/fmars.2018.00125| doi-access=free | bibcode=2018FrMaS...5..125H }} [[File:CC-BY icon.svg|50px]] Modified material was copied from this source, which is available under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License].</ref>

The process of building a mineral-based cell wall inside the cell, then exporting it outside, is a massive event that must involve large numbers of genes and their protein products. The act of building and [[exocytosing]] this large structural object in a short time period, synched with [[cell cycle]] progression, necessitates substantial physical movements within the cell as well as dedication of a significant proportion of the cell's [[biosynthetic]] capacities.<ref name=Hildebrand2018 />

The first characterisations of the biochemical processes and components involved in diatom silicification were made in the late 1990s.<ref>{{cite journal | last1=Hildebrand | first1=Mark | last2=Volcani | first2=Benjamin E. | last3=Gassmann | first3=Walter | last4=Schroeder | first4=Julian I. | title=A gene family of silicon transporters | journal=Nature | publisher=Springer Science and Business Media LLC | volume=385 | issue=6618 | year=1997 | issn=0028-0836 | doi=10.1038/385688b0 | pages=688–689| pmid=9034185 | bibcode=1997Natur.385..688H | s2cid=4266966 }}</ref><ref>{{cite journal | last1=Kröger | first1=Nils | last2=Deutzmann | first2=Rainer | last3=Sumper | first3=Manfred | title=Polycationic Peptides from Diatom Biosilica That Direct Silica Nanosphere Formation | journal=Science | publisher=American Association for the Advancement of Science (AAAS) | volume=286 | issue=5442 | date=1999-11-05 | issn=0036-8075 | doi=10.1126/science.286.5442.1129 | pages=1129–1132| pmid=10550045 }}</ref><ref>{{cite journal | last1=Kröger | first1=Nils | last2=Deutzmann | first2=Rainer | last3=Bergsdorf | first3=Christian | last4=Sumper | first4=Manfred | title=Species-specific polyamines from diatoms control silica morphology | journal=Proceedings of the National Academy of Sciences | volume=97 | issue=26 | date=2000-12-05 | issn=0027-8424 | doi=10.1073/pnas.260496497 | pages=14133–14138| pmid=11106386 | pmc=18883 | bibcode=2000PNAS...9714133K | doi-access=free }}</ref> These were followed by insights into how higher order assembly of silica structures might occur.<ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Hildebrand | first2=Mark | title=Extensive and Intimate Association of the Cytoskeleton with Forming Silica in Diatoms: Control over Patterning on the Meso- and Micro-Scale | journal=PLOS ONE | publisher=Public Library of Science (PLoS) | volume=5 | issue=12 | date=2010-12-10 | issn=1932-6203 | doi=10.1371/journal.pone.0014300 | page=e14300| pmid=21200414 | pmc=3000822 | bibcode=2010PLoSO...514300T | doi-access=free }}</ref><ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Hildebrand | first2=Mark | title=Characterization and Localization of Insoluble Organic Matrices Associated with Diatom Cell Walls: Insight into Their Roles during Cell Wall Formation | journal=PLOS ONE | publisher=Public Library of Science (PLoS) | volume=8 | issue=4 | date=2013-04-23 | issn=1932-6203 | doi=10.1371/journal.pone.0061675 | page=e61675| pmid=23626714 | pmc=3633991 | bibcode=2013PLoSO...861675T | doi-access=free }}</ref><ref>{{cite journal | last1=Scheffel | first1=André | last2=Poulsen | first2=Nicole | last3=Shian | first3=Samuel | last4=Kröger | first4=Nils | title=Nanopatterned protein microrings from a diatom that direct silica morphogenesis | journal=Proceedings of the National Academy of Sciences | volume=108 | issue=8 | date=2011-02-07 | issn=0027-8424 | doi=10.1073/pnas.1012842108 | pages=3175–3180| pmid=21300899 | pmc=3044418 | doi-access=free }}</ref> More recent reports describe the identification of novel components involved in higher order processes, the dynamics documented through real-time imaging, and the genetic manipulation of silica structure.<ref>{{cite journal | last1=Kotzsch | first1=Alexander | last2=Gröger | first2=Philip | last3=Pawolski | first3=Damian | last4=Bomans | first4=Paul H. H. | last5=Sommerdijk | first5=Nico A. J. M. | last6=Schlierf | first6=Michael | last7=Kröger | first7=Nils | title=Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization | journal=BMC Biology | publisher=Springer Science and Business Media LLC | volume=15 | issue=1 | date=2017-07-24 | page=65 | issn=1741-7007 | doi=10.1186/s12915-017-0400-8| pmid=28738898 | pmc=5525289 | doi-access=free }}</ref><ref>{{cite journal | last1=Tesson | first1=Benoit | last2=Lerch | first2=Sarah J. L. | last3=Hildebrand | first3=Mark | title=Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica | journal=Scientific Reports | publisher=Springer Science and Business Media LLC | volume=7 | issue=1 | date=2017-10-18 | page=13457 | issn=2045-2322 | doi=10.1038/s41598-017-13613-8| pmid=29044150 | pmc=5647440 | bibcode=2017NatSR...713457T }}</ref> The approaches established in these recent works provide practical avenues to not only identify the components involved in silica cell wall formation but to elucidate their interactions and spatio-temporal dynamics. This type of holistic understanding will be necessary to achieve a more complete understanding of cell wall synthesis.<ref name=Hildebrand2018 />