Global InformationSecondary chromosome information
Chromids,[1] formerly (and less specifically) secondary chromosomes,[a] are a class of bacterial replicons (replicating DNA molecules). These replicons are called "chromids" because they have characteristic features of both chromosomes and plasmids. Early on, it was thought that all core genes could be found on the main chromosome of the bacteria. However, in 1989 a replicon (now known as a chromid) was discovered containing core genes outside of the main chromosome. These core genes make the chromid indispensable to the organism. Chromids are large replicons, although not as large as the main chromosome. However, chromids are almost always larger than a plasmid (or megaplasmid). Chromids also share many genomic signatures of the chromosome, including their GC-content and their codon usage bias. On the other hand, chromids do not share the replication systems of chromosomes. Instead, they use the replication system of plasmids. Chromids are present in 10% of bacteria species sequenced by 2009.[5]
Bacterial genomes divided between a main chromosome and one or more chromids (and / or megaplasmids) are said to be divided or multipartite genomes. The vast majority of chromid-encoding bacteria only have a single chromid, although 9% have more than one (compared with 12% of megaplasmid-encoding bacteria containing multiple megaplasmids). The genus Azospirillum contains three species which have up to five chromids, the most chromids known in a single species to date. Chromids also appear to be more common in bacteria which have a symbiotic or pathogenic relationship with eukaryotes[6] and with organisms with high tolerance to abiotic stressors.[7]
Chromids were discovered in 1989, in a species of Alphaproteobacteria known as Rhodobacter sphaeroides.[8] However, the formalization of the concept of a "chromid" as an independent type of replicon only came about in 2010.[1] Several classifications further distinguish between chromids depending on conditions of their essentiality, their replication system, and more.
The two hypotheses for the origins of chromids are the "plasmid" and "schism" hypotheses. According to the plasmid hypothesis, chromids originate from plasmids which have acquired core genes over evolutionary time and so stabilized in their respective lineages. According to the schism hypothesis, chromids as well as the main chromosome originate from a schism of a larger, earlier chromosome. The plasmid hypothesis is presently widely accepted, although there may be rare cases where large replicons originate from a chromosomal schism. One finding holds that chromids originated 45 times across bacterial phylogenies and were lost twice.[6]
- ^ a b Fournes, Florian; Val, Marie-Eve; Skovgaard, Ole; Mazel, Didier (2018). "Replicate Once Per Cell Cycle: Replication Control of Secondary Chromosomes". Frontiers in Microbiology. 9: 1833. doi:10.3389/fmicb.2018.01833. ISSN 1664-302X. PMC 6090056. PMID 30131796.
- ^ DelVecchio, VG; Kapatral, V; Redkar, RJ; Patra, G; Mujer, C; Los, T; Ivanova, N; Anderson, I; Bhattacharyya, A; Lykidis, A; Reznik, G; Jablonski, L; Larsen, N; D'Souza, M; Bernal, A; Mazur, M; Goltsman, E; Selkov, E; Elzer, PH; Hagius, S; O'Callaghan, D; Letesson, JJ; Haselkorn, R; Kyrpides, N; Overbeek, R (8 January 2002). "The genome sequence of the facultative intracellular pathogen Brucella melitensis". Proceedings of the National Academy of Sciences of the United States of America. 99 (1): 443–8. Bibcode:2002PNAS...99..443D. doi:10.1073/pnas.221575398. PMC 117579. PMID 11756688.
- ^ Krzyżanowska, DM; Maciąg, T; Ossowicki, A; Rajewska, M; Kaczyński, Z; Czerwicka, M; Rąbalski, Ł; Czaplewska, P; Jafra, S (2019). "Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains". PLOS ONE. 14 (1): e0210874. doi:10.1371/journal.pone.0210874. PMC 6342446. PMID 30668584.
- ^ Ausiannikava, D; Mitchell, L; Marriott, H; Smith, V; Hawkins, M; Makarova, KS; Koonin, EV; Nieduszynski, CA; Allers, T (1 August 2018). "Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii". Molecular Biology and Evolution. 35 (8): 1855–1868. doi:10.1093/molbev/msy075. PMC 6063281. PMID 29668953.
- ^ Harrison, Peter W.; Lower, Ryan P.J.; Kim, Nayoung K.D.; Young, J. Peter W. (2010). "Introducing the bacterial 'chromid': not a chromosome, not a plasmid". Trends in Microbiology. 18 (4): 141–148. doi:10.1016/j.tim.2009.12.010. PMID 20080407.
- ^ a b diCenzo, George C.; Finan, Turlough M. (2017-08-09). "The Divided Bacterial Genome: Structure, Function, and Evolution". Microbiology and Molecular Biology Reviews. 81 (3). doi:10.1128/MMBR.00019-17. PMC 5584315. PMID 28794225.
- ^ Sonnenberg, Cecilie Bækkedal; Haugen, Peik (2021-09-01). "The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid". G3: Genes, Genomes, Genetics. 11 (9): jkab256. doi:10.1093/g3journal/jkab256. ISSN 2160-1836. PMC 8496264. PMID 34544144.
- ^ Suwanto, A; Kaplan, S (1989). "Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes". Journal of Bacteriology. 171 (11): 5850–5859. doi:10.1128/jb.171.11.5850-5859.1989. ISSN 0021-9193. PMC 210445. PMID 2808300.
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