Editing Vibrio cholerae (section)

==Genome==
''V. cholerae'' (and [[Vibrionaceae]] in general)<ref name=Bruhn>{{cite journal |last1=Bruhn |first1=Matthias |last2=Schindler |first2=Daniel |last3=Kemter |first3=Franziska S. |last4=Wiley |first4=Michael R. |last5=Chase |first5=Kitty |last6=Koroleva |first6=Galina I. |last7=Palacios |first7=Gustavo |last8=Sozhamannan |first8=Shanmuga |last9=Waldminghaus |first9=Torsten |title=Functionality of Two Origins of Replication in Vibrio cholerae Strains With a Single Chromosome |journal=Frontiers in Microbiology |date=30 November 2018 |volume=9 |pages=2932 |doi=10.3389/fmicb.2018.02932|pmid=30559732 |pmc=6284228 |doi-access=free }}</ref> has two circular [[chromosomes]], together totalling 4 million [[base pairs]] of [[DNA]] sequence and 3,885 predicted [[genes]].<ref>{{cite journal |last1=Fraser |first1=Claire M. |last2=Heidelberg |first2=John F. |last3=Eisen |first3=Jonathan A. |last4=Nelson |first4=William C. |last5=Clayton |first5=Rebecca A. |last6=Gwinn |first6=Michelle L. |last7=Dodson |first7=Robert J. |last8=Haft |first8=Daniel H. |last9=Hickey |first9=Erin K. |title=DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae |journal=Nature |volume=406 |issue=6795 |pages=477–83 |year=2000 |pmid=10952301 |pmc=8288016 |doi=10.1038/35020000 |display-authors=8 |last10=Umayam |first10=L. |last11=Gill |first11=S.R. |last12=Nelson |first12=K.E. |last13=Read |first13=T.D. |last14=Tettelin |first14=H. |last15=Richardson |first15=D. |last16=Ermolaeva |first16=M.D. |last17=Vamathevan |first17=J. |last18=Bass |first18=S. |last19=Qin |first19=H. |last20=Dragoi |first20=I. |last21=Sellers |first21=P. |last22=McDonald |first22=L. |last23=Utterback |first23=T. |last24=Fleishmann |first24=R.D. |last25=Nierman |first25=W.C. |last26=White |first26=O. |last27=Salzberg |first27=S.L. |last28=Smith |first28=H.O. |last29=Colwell |first29=R.R. |last30=Mekalanos |first30=J.J. |bibcode=2000Natur.406..477H |s2cid=807509 |url=http://www.nature.com/nature/journal/v406/n6795/pdf/406477aa.pdf |doi-access=free |access-date=2018-04-20 |archive-date=2021-12-19 |archive-url=https://web.archive.org/web/20211219124913/https://www.nature.com/nature/journal/v406/n6795/pdf/406477aa.pdf |url-status=live }}</ref>  The genes for cholera toxin are carried by CTXphi (CTXφ), a [[temperateness (virology)|temperate]] [[bacteriophage]] inserted into the ''V. cholerae'' genome. CTXφ can transmit cholera toxin genes from one ''V. cholerae'' strain to another, one form of [[horizontal gene transfer]]. The genes for toxin coregulated pilus are coded by the Vibrio [[pathogenicity island]] (VPI), which is separate from the [[prophage]].<ref name="cdc.gov" />

The larger first chromosome is 3&nbsp;Mbp long with 2,770 [[open reading frame]]s (ORFs). It contains the crucial genes for toxicity, regulation of toxicity, and important cellular functions, such as [[Transcription (genetics)|transcription]] and [[Translation (biology)|translation]].<ref name=cdc.gov />

The second chromosome is 1&nbsp;Mbp long with 1115 ORFs. It is determined to be different from a [[plasmid]] or [[megaplasmid]] due to the inclusion of housekeeping and other essential genes in the genome, including essential genes for metabolism, heat-shock proteins, and [[MT-RNR2|16S rRNA]] genes, which are ribosomal subunit genes used to track evolutionary relationships between bacteria. Also relevant in determining if the [[replicon (genetics)|replicon]] is a chromosome is whether it represents a significant percentage of the genome, and chromosome 2 is 40% by size of the entire genome. And, unlike plasmids, chromosomes are not self-transmissible.<ref name="jones1984" /> However, the second chromosome may have once been a megaplasmid because it contains some genes usually found on plasmids,<ref name=cdc.gov /> including a P1 plastid-like [[origin of replication]].<ref name=Bruhn/>

===Bacteriophage CTXφ===
[[CTXφ bacteriophage|CTXφ]] (also called CTXphi) is a [[filamentous phage]] that contains the genes for [[cholera toxin]]. Infectious CTXφ particles are produced when ''V. cholerae'' infects humans. Phage particles are secreted from bacterial cells without [[lysis]]. When CTXφ infects ''V. cholerae'' cells, it integrates into specific sites on either chromosome. These sites often contain [[tandem array]]s of integrated CTXφ [[prophage]]. In addition to the ''ctxA'' and ''ctxB'' genes encoding cholera toxin, CTXφ contains eight genes involved in phage reproduction, packaging, secretion, integration, and regulation. The CTXφ genome is 6.9 kb long.<ref>{{cite journal |last1=McLeod |first1=S. M. |last2=Kimsey |first2=H. H. |last3=Davis |first3=B. M. |last4=Waldor |first4=M. K. |title=CTXφ and ''Vibrio cholerae'': exploring a newly recognized type of phage-host cell relationship |journal=Molecular Microbiology |volume=57 |issue=2 |pages=347–356 |year=2005 |pmid=15978069 |doi=10.1111/j.1365-2958.2005.04676.x |doi-access=free }}</ref>