Editing Mycobacterium smegmatis

{{Short description|Species of bacterium}}
{{Speciesbox
| image = Mycobacterium_smegmatis.tif
| taxon = Mycobacterium smegmatis
| authority = (Trevisan 1889)<br>Lehmann &amp; Neumann 1899
}}

'''''Mycobacterium smegmatis''''' is an [[acid-fast]] [[bacterium|bacterial]] species in the [[phylum]] ''[[Actinomycetota]]'' and the [[genus]] ''[[Mycobacterium]]''.  It is 3.0 to 5.0&nbsp;μm long with a [[bacillus (shape)|bacillus]] shape and can be stained by Ziehl–Neelsen method and the auramine-rhodamine fluorescent method. It was first reported in November 1884, who found a [[bacillus]] with the staining appearance of tubercle bacilli in [[syphilis|syphilitic]] [[chancres]].  Subsequent to this, Alvarez and Tavel found organisms similar to that described by Lustgarten also in normal [[genital]] [[secretions]] ([[smegma]]). This organism was later named ''M. smegmatis''.<ref>{{cite journal | vauthors = Gordon RE, Smith MM | title = Rapidly growing, acid fast bacteria. I. Species' descriptions of Mycobacterium phlei Lehmann and Neumann and Mycobacterium smegmatis (Trevisan) Lehmann and Neumann | journal = Journal of Bacteriology | volume = 66 | issue = 1 | pages = 41–8 | date = July 1953 | pmid = 13069464 | pmc = 357089 | doi = 10.1128/jb.66.1.41-48.1953 }}</ref>

Some species of the genus ''Mycobacterium'' have recently been renamed to ''[[Mycolicibacterium]]'', so that ''M. smegmatis'' is now ''Mycolicibacterium smegmatis''.<ref>{{cite journal |vauthors=Gupta RS, Lo B, Son J |title=Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus ''Mycobacterium'' into an Emended Genus ''Mycobacterium'' and Four Novel Genera |language=English |journal=Frontiers in Microbiology |volume=9 |pages=67 |date=2018 |pmid=29497402 |pmc=5819568 |doi=10.3389/fmicb.2018.00067 |doi-access=free}}</ref><ref>{{Cite web|last=taxonomy|title=Taxonomy browser (Mycolicibacterium smegmatis) |url= https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1772&lvl=3&lin=f&keep=1&srchmode=1&unlock |access-date=2021-06-16|website=www.ncbi.nlm.nih.gov}}</ref>

''M. smegmatis'', which was previously considered a nonmotile organism, uses a sliding mechanism that allows it to move around its environment. Henrichsen<ref>{{Cite journal |last=Henrichsen |first=J |date=1972-12-01 |title=Bacterial surface translocation: a survey and a classification |journal=Bacteriological Reviews |language=en |volume=36 |issue=4 |pages=478–503 |doi=10.1128/br.36.4.478-503.1972 |doi-access=free |issn=0005-3678 |pmc=408329 |pmid=4631369}}</ref> defines it as, “a kind of surface translocation produced by the expansive forces in a growing culture in combination with special surface properties of the cells resulting in reduced friction between cell and substrate”. Essentially, the bacteria form a single-layered sheet and are able to move slowly together without the use of any extracellular structures, like flagella or pili. Although it hasn’t been determined exactly how this mechanism works, the surface properties of the unique cell wall of ''M. smegmatis'' have been found to play a role. For example, this sliding ability is correlated with the presence of glycopeptidolipids (GPLs) on the outermost part of the cell wall. GPLs are amphiphilic molecules that could potentially decrease surface interactions or create a conditioning film that allows movement. Although the exact role of GPLs in sliding is not known, without them ''M. smegmatis'' does not have the ability to translocate.<ref>{{Cite journal |last1=Martínez |first1=Asunción |last2=Torello |first2=Sandra |last3=Kolter |first3=Roberto |date=1999-12-01 |title=Sliding Motility in Mycobacteria |journal=Journal of Bacteriology |language=en |volume=181 |issue=23 |pages=7331–7338 |doi=10.1128/JB.181.23.7331-7338.1999 |doi-access=free |issn=0021-9193 |pmc=103697 |pmid=10572138}}</ref>

[[File:M. smegmatis plaque.jpg|thumb|[[Viral plaque|Plaques]] from a [[virus]] isolated from a [[compost]] heap near [[UCLA]]. The [[bacterium]] is ''M. smegmatis'']]

==Virulence==
''M. smegmatis'' is generally considered a non-pathogenic microorganism; however, in some very rare cases, it may cause disease.<ref>{{cite journal |vauthors=Reyrat JM, Kahn D |title=Mycobacterium smegmatis: an absurd model for tuberculosis? |journal=Trends in Microbiology |volume=9 |issue=10 |pages=472–474 |date=October 2001 |pmid=11597444 |doi=10.1016/S0966-842X(01)02168-0}}</ref>

== Genetics and genomics ==
The genomes of multiple strains of ''M. smegmatis'' have been sequenced by [[J. Craig Venter Institute|TIGR]] and other laboratories, including the "wild-type" (mc<sup>2</sup> 155) and some antibiotic-resistant strains (4XR1/R2).<ref>{{cite journal | vauthors = Mohan A, Padiadpu J, Baloni P, Chandra N | title = Complete Genome Sequences of a Mycobacterium smegmatis Laboratory Strain (MC2 155) and Isoniazid-Resistant (4XR1/R2) Mutant Strains | journal = Genome Announcements | volume = 3 | issue = 1 | date = February 2015 | pmid = 25657281 | pmc = 4319614 | doi = 10.1128/genomeA.01520-14 }}</ref> The genome of strain mc<sup>2</sup>155 is ~6,9 Mbp long and encodes ~6400 proteins<ref>{{Cite web|title=Mycolicibacterium smegmatis (ID 1026) - Genome - NCBI|url=https://www.ncbi.nlm.nih.gov/genome/?term=txid1772%5BOrganism:exp%5D|access-date=2021-06-16|website=www.ncbi.nlm.nih.gov}}</ref> which is relatively large for bacteria (for comparison, the genome of [[Escherichia coli|E. coli]] encodes about 4000 proteins).

This species shares more than 2000 homologous genes with ''M. tuberculosis'' and thus is a good model organism to study mycobacteria in general and the highly pathogenic ''M. tuberculosis'' in particular; however, only 12 of the 19 virulence genes in ''M. tuberculosis'' have homologues in ''M. smegmatis''.<ref>{{cite journal |last1=Reyrat |first1=Jean-Marc |last2=Kahn |first2=Daniel |title=Mycobacterium smegmatis: an absurd model for tuberculosis? |journal=Trends in Microbiology |date=October 2001 |volume=9 |issue=10 |pages=472–473 |doi=10.1016/S0966-842X(01)02168-0}}</ref><ref>{{cite journal |last1=Camacho |first1=Luis Reinaldo |last2=Ensergueix |first2=Danielle |last3=Perez |first3=Esther |last4=Gicquel |first4=Brigitte |last5=Guilhot |first5=Christophe |title=Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis |journal=Molecular Microbiology |date=October 1999 |volume=34 |issue=2 |pages=257–267 |doi=10.1046/j.1365-2958.1999.01593.x|doi-access=free }}</ref><ref>{{cite journal |last1=Glickman |first1=Michael S |last2=Cox |first2=Jeffery S |last3=Jacobs |first3=William R |title=A Novel Mycolic Acid Cyclopropane Synthetase Is Required for Cording, Persistence, and Virulence of Mycobacterium tuberculosis |journal=Molecular Cell |date=April 2000 |volume=5 |issue=4 |pages=717–727 |doi=10.1016/s1097-2765(00)80250-6|doi-access=free }}</ref><ref>{{cite journal |last1=Berthet |first1=François-Xavier |last2=Lagranderie |first2=Micheline |last3=Gounon |first3=Pierre |last4=Laurent-Winter |first4=Christine |last5=Ensergueix |first5=Danielle |last6=Chavarot |first6=Pierre |last7=Thouron |first7=Françoise |last8=Maranghi |first8=Eddie |last9=Pelicic |first9=Vladimir |last10=Portnoı̈ |first10=Denis |last11=Marchal |first11=Gilles |last12=Gicquel |first12=Brigitte |title=Attenuation of Virulence by Disruption of the Mycobacterium tuberculosis erp Gene |journal=Science |date=23 October 1998 |volume=282 |issue=5389 |pages=759–762 |doi=10.1126/science.282.5389.759}}</ref>

The discovery of [[plasmid]]s, [[bacteriophage|phages]], and [[mobile genetic elements]] has enabled the construction of dedicated gene-inactivation and gene reporter systems. The ''M. smegmatis'' mc<sup>2</sup>155 strain is hypertransformable, and is now the work-horse of mycobacterial genetics.{{cn|date=April 2023}}

===Transformation===
Transformation is a process by which a bacterial cell takes up DNA that had been released by another cell into the surrounding medium, and then incorporates that DNA into its own genome by homologous recombination (see [[Transformation (genetics)]]).  Strains of ''M. smegmatis'' that have particularly efficient DNA repair machinery, as indicated by their greater resistance to the DNA damaging effects of agents such as UV and mitomycin C, proved to be the most capable of undergoing transformation.<ref name="pmid641008">{{cite journal | vauthors = Norgard MV, Imaeda T | title = Physiological factors involved in the transformation of Mycobacterium smegmatis | journal = Journal of Bacteriology | volume = 133 | issue = 3 | pages = 1254–62 | date = March 1978 | pmid = 641008 | pmc = 222159 | doi = 10.1128/jb.133.3.1254-1262.1978 }}</ref>  This suggests that transformation in ''M. smegmatis'' is a DNA repair process, presumably a recombinational repair process, as it is in other bacterial species.<ref name="pmid18295550">{{cite journal | vauthors = Michod RE, Bernstein H, Nedelcu AM | title = Adaptive value of sex in microbial pathogens | journal = Infection, Genetics and Evolution | volume = 8 | issue = 3 | pages = 267–85 | date = May 2008 | pmid = 18295550 | doi = 10.1016/j.meegid.2008.01.002 }}</ref>

===Conjugation===
Conjugal DNA transfer in ''M. smegmatis'' requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient’s chromosome by homologous recombination.  However, in contrast to the well-known ''E. coli'' Hfr conjugation system, in ''M. smegmatis'' all regions of the chromosome are transferred with comparable efficiencies and mycobacterial conjugation is chromosome, rather than plasmid based.  Gray et al.<ref name="pmid23874149">{{cite journal | vauthors = Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM | title = Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus | journal = PLOS Biology | volume = 11 | issue = 7 | pages = e1001602 | date = July 2013 | pmid = 23874149 | pmc = 3706393 | doi = 10.1371/journal.pbio.1001602 | doi-access = free }}</ref> reported substantial blending of the parental genomes resulting from conjugation and referred to this blending as reminiscent of that seen in the meiotic products of sexual reproduction (see [[Evolution of sexual reproduction#Origin of sexual reproduction|Origin of sexual reproduction]]).{{cn|date=April 2023}}

==DNA repair==
''Mycobacterium smegmatis'' relies on [[DNA repair]] pathways to resist DNA damage. Double-strand breaks are especially threatening to bacterial viability.  ''M. smegmatis'' has three options for repairing double-strand breaks; [[homologous recombination]] (HR), [[non-homologous end joining]] (NHEJ), and [[Homologous recombination#SSA pathway|single-strand annealing (SSA)]].<ref name=Gupta>{{cite journal | vauthors = Gupta R, Barkan D, Redelman-Sidi G, Shuman S, Glickman MS | title = Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways | journal = Molecular Microbiology | volume = 79 | issue = 2 | pages = 316–30 | date = January 2011 | pmid = 21219454 | pmc = 3812669 | doi = 10.1111/j.1365-2958.2010.07463.x }}</ref>  The HR pathway of ''M. smegmatis'' is the major determinant of resistance to ionizing radiation and oxidative DNA damage.  This pathway involves exchange of information between a damaged chromosome and another homologous chromosome in the same cell.  It depends on the RecA protein that catalyzes strand exchange and the ADN protein that acts as a presynaptic nuclease.<ref name=Gupta />  HR is an accurate repair process and is the preferred pathway during logarithmic growth.<ref name=Pitcher>{{cite journal | vauthors = Pitcher RS, Green AJ, Brzostek A, Korycka-Machala M, Dziadek J, Doherty AJ | title = NHEJ protects mycobacteria in stationary phase against the harmful effects of desiccation | journal = DNA Repair | volume = 6 | issue = 9 | pages = 1271–6 | date = September 2007 | pmid = 17360246 | doi = 10.1016/j.dnarep.2007.02.009 | url = http://sro.sussex.ac.uk/id/eprint/1122/1/DNA_Doherty.pdf }}</ref>

The NHEJ pathway for repairing double-strand breaks involves the rejoining of the broken ends. It does not depend on a second homologous chromosome.  This pathway requires the [[Ku (protein)|Ku protein]] and a specialized poly-functional ATP-dependent DNA ligase (ligase D).<ref name=Gong>{{cite journal | vauthors = Gong C, Bongiorno P, Martins A, Stephanou NC, Zhu H, Shuman S, Glickman MS | title = Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C | journal = Nature Structural & Molecular Biology | volume = 12 | issue = 4 | pages = 304–12 | date = April 2005 | pmid = 15778718 | doi = 10.1038/nsmb915 | s2cid = 6879518 }}</ref>  NHEJ is efficient but inaccurate.  Sealing of blunt DNA ends within a functional gene sequence occurs with a mutation frequency of about 50%.<ref name=Gong />  NHEJ is the preferred pathway during stationary phase, and it protects ''M. smegmatis'' against the harmful effects of desiccation.<ref name=Pitcher />

SSA is employed as a repair pathway when a double-strand break arises between direct repeat sequences in DNA.  SSA involves single-strand resection, annealing of the repeats, flap removal, gap filling and ligation.  In ''M. smegmatis'' the SSA pathway depends on the RecBCD helicase-nuclease.<ref name=Gupta />

==Applications==
===Use in research===
''Mycobacterium smegmatis'' is useful for the research analysis of other ''Mycobacteria'' species in laboratory experiments.  ''M. smegmatis'' is commonly used in work on the ''Mycobacterium'' genus due to it being a "fast grower" and non-pathogenic. ''M. smegmatis'' is a simple model that is easy to work with, i.e., with a fast [[doubling time]] and only requires a [[biosafety level]] 1 laboratory.  The time and heavy infrastructure needed to work with pathogenic species prompted researchers to use ''M. smegmatis'' as a model for mycobacterial species.{{cn|date=April 2023}}

''Mycobacterium smegmatis'' shares the same peculiar cell wall structure of [[Mycobacterium tuberculosis|''M. tuberculosis'']] and other mycobacterial species.<ref>{{cite journal |vauthors=King GM |title=Uptake of carbon monoxide and hydrogen at environmentally relevant concentrations by mycobacteria |journal=Applied and Environmental Microbiology |volume=69 |issue=12 |pages=7266–7272 |date=December 2003 |pmid=14660375 |pmc=310020 |doi=10.1128/aem.69.12.7266-7272.2003}}</ref> It is also capable of oxidizing carbon monoxide aerobically, as is ''M. tuberculosis.''{{cn|date=April 2023}}

Bacterial secretion systems are specialized protein complexes and pathways that allow bacterial pathogens to secrete proteins across their cell membranes and, ultimately, to host cells. These effector proteins are important virulence factors, which allow the pathogen to survive inside of the host. There are many different kinds of specific secretion systems, and ''M. tuberculosis'' has an Snm (secretion in mycobacteria) protein secretion system, now called the ESX secretion system. Although the ESX secretion system is a key in determining ''M. tuberculosis'' virulence, all mycobacteria have genes encoding the components of this system. This area of the genome is referred to as the RD1 locus. ''M. smegmatis'' is commonly used to study ESX secretion because of its genetic similarities  and analogous function to ''M. tuberculosis'', as well as ease of growing in the lab. One example of how this can be applied in research is the identification of gene products required for ESX secretion. By knocking out genes in the RD1 locus of ''M. smegmatis'' and testing efficiency of ESX secretion before and after gene knockout, specific genes can be identified as necessary for ESX secretion. These findings can be applied to the ESX secretion system of ''M. tuberculosis''.<ref>{{Cite journal |last1=Converse |first1=Scott E. |last2=Cox |first2=Jeffery S. |date=2005-02-15 |title=A Protein Secretion Pathway Critical for Mycobacterium tuberculosis Virulence Is Conserved and Functional in Mycobacterium smegmatis |journal=Journal of Bacteriology |language=en |volume=187 |issue=4 |pages=1238–1245 |doi=10.1128/JB.187.4.1238-1245.2005 |issn=0021-9193 |pmc=545616 |pmid=15687187}}</ref>

''Mycobacterium smegmatis'' is readily cultivatable in most synthetic or complex laboratory media, where it can form visible colonies in 3–5 days. These properties make it a very attractive model organism for ''M. tuberculosis'' and other mycobacterial pathogens. ''M. smegmatis'' mc<sup>2</sup>155 is also used for the cultivation of [[mycobacteriophage]].{{cn|date=April 2023}}

===Production of electricity===
{{See also|Electric bacteria}}
Like many other bacteria, ''M. smegmatis'' is known to use the trace levels of [[hydrogen]] in the [[atmosphere]] as an energy source. In 2023, researchers reported extracting from ''M. smegmatis'' a [[hydrogenase]] called [[Huc (hydrogenase)|Huc]], which is highly efficient at [[oxidation|oxidizing]] hydrogen gas—and thus creating an [[electric current]]—while also being insensitive to the presence of [[oxygen]], which typically obstructs [[catalysis]].<ref>{{cite journal | last1 = Grinter | first1 = R. | last2 = Kropp | first2 = A. | last3 = Venugopal | display-authors=etal | title = Structural basis for bacterial energy extraction from atmospheric hydrogen | journal = Nature | date = 2023 | volume = 615 | issue = 7952 | pages = 541–547 | doi = 10.1038/s41586-023-05781-7| doi-access = free | pmc = 10017518 }}</ref> This discovery offers significant potential for [[green energy]].{{cn|date=April 2023}}

== References ==
{{Reflist}}

== External links ==
* [https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=92 Information and photo from NCBI]
* [http://microbewiki.kenyon.edu/index.php/Mycobacterium_smegmatis MicrobeWiki page on M. smegmatis]
* [http://bacdive.dsmz.de/index.php?search=8324&submit=Search Type strain of ''Mycobacterium smegmatis'' at Bac''Dive'' -  the Bacterial Diversity Metadatabase]

{{Mycobacteria}}

{{Taxonbar|from=Q606230}}

[[Category:Nontuberculous mycobacteria|smegmatis]]
[[Category:Bacteria described in 1899]]