Secondary chromosome
Chromids, formerly secondary chromosomes, are a class of bacterial replicons. 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 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. 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.
Bacterial genomes divided between a main chromosome and one or more chromids 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. 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 and with organisms with high tolerance to abiotic stressors.
Chromids were discovered in 1989, in a species of Alphaproteobacteria known as Rhodobacter sphaeroides. However, the formalization of the concept of a "chromid" as an independent type of replicon only came about in 2010. 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.
Discovery and classification
Discovery
Early in the era of bacterial genomics, the genomes of bacteria were thought to have a relatively simple architecture. All known bacteria had circular chromosomes containing all the crucial genes. Some bacteria had additional replicons known as plasmids, and plasmids were characteristically small, circular, and dispensable. As more bacteria and their genomes were studied, many alternative forms of bacterial genomic architecture began to be discovered. Linear chromosomes and linear plasmids were discovered in a number of species. Soon after, bacteria with several large replicons were discovered, leading to the view that bacteria, just like eukaryotes, can have a genome made up of more than one chromosome. The first example of this was Rhodobacter sphaeroides in 1989, but additional discoveries quickly followed with Brucella melitensis in 1993, Burkholderia cepacia complex in 1994, Rhizobium meliloti in 1995, Bacillus thuringiensis in 1996, and now about 10% of bacterial species are known to have large replicons that are separate from the main chromosome.Definition
With the onset of these discoveries, several approaches in classifying different components of multipartite genomes were proposed. Various terms have been used to describe large replicons other than the main chromosome, including simply designating them as additional chromosomes, or "minichromosomes", "megaplasmids", or "secondary chromosomes". Criteria used to distinguish between these replicons typically revolve around features such as size and the presence of core genes. In 2010, the classification of these genomic elements as chromids was proposed. Previous terms, such as "secondary chromosome", are considered inadequate upon the observation that these replicons contain the replication systems of plasmids and so are a fundamentally different class of replicons than chromosomes. The original definition of a 'chromid' involves meeting three criteria:While this definition is robust, the authors who proposed it did so with the expectation that some exceptions would be found that would blur the lines between chromids and other replicons. This expectation existed because of the general tendency for evolutionary lineages to produce ambiguous systems, which has resulted in the more well-known issues in formulating a widely encompassing species definition.
Since the classification of chromids, other replicons have been discovered which share some features of chromids but have been categorized separately. One example is the designated "rrn-plasmid" found in a clade within the bacterial genus Aureimonas. The rrn-plasmid contains the rrn operon, and the rrn operon cannot be found on the main chromosome. The main chromosome is therefore termed as an "rrn-lacking chromosome" or RLC, and so the clade of bacteria within Aureimonas which possess the rrn-plasmid is also termed the "RLC clade". Members of the RLC clade have nine replicons, of which the main chromosome is the largest and the rrn-plasmid is the smallest at only 9.4kb. The rrn-plasmid also has a high copy number in RLC bacteria. While this very small size and copy number resembles plasmids more than it does chromids, the rrn-plasmid still ahs the only copies of the genes in the rrn operon and for tRNA. This distinctive collection of features led the scientists discovering this replicon to simply classify it as an rrn-plasmid, which is thought of as a separate classification than a "plasmid" or "chromid".
Additional proposed classifications
Beyond classifying certain replicons as chromids, a number of scientists have proposed further distinguishing between different types of chromids. One classification distinguishes between primary and secondary chromids. Primary chromids are defined as chromids containing core genes that are always essential for the survival of the bacterium under all conditions. Secondary chromids are defined as chromids essential for survival in the native conditions of the bacterium, but may be non-essential in certain "safe" conditions such as a laboratory environment. Secondary chromids may also have more recent evolutionary origins and may retain some more plasmid-like features as compared with primary chromids. An example of a proposed primary chromid is "chromosome II" of Paracoccus denitrificans PD1222.Characteristics
Size and copy number
In a bacterial genome, the main chromosome will always be the largest replicon, followed by the chromid and then the plasmid. One exception to this trend is known in Deinococcus deserti VCD115, where both plasmids are larger than the chromid.Chromids vary considerably in size between organisms. In the bacterial genus Vibrio, the main chromosome varies between 3.0 and 3.3 Mb whereas the chromid varies between 0.8 and 2.4 Mb in size. A replicon in a strain of Buchnera, which encodes some core genes, is only 7.8kb. While the presence of core genes may lead to the classification of this replicon as a chromid, this replicon may also be excluded on certain definitions. Some approaches only categorize certain replicons as chromids if they meet a threshold size of 350kb. It has also been observed that chromids tend to have a low copy number in the cell, as with chromosomes and megaplasmids. On average, chromids are twice as large as megaplasmids. One of the largest chromids is the one in Burkholderia pseudomallei, which exceeds 3.1 million nucleotides in size, i.e. 3.1 megabases or 3.1 Mb.
Genomic features
Chromids more frequently have a lower G + C content compared with the main chromosome, although the strength of this association is not very strong. A chromid will also typically have a G + C content within 1% of that of the main chromosome, reflecting its nearing the base composition equilibrium of the main chromosome after having stably existed within a bacterial lineage for a necessary period of time. Chromids also resemble the main chromosome in their codon usage bias. One analysis found that chromids had a median 0.34% difference in GC content with the main chromosome, compared with values of 1.9% for megaplasmids and 2.8% for plasmids.Chromids have at least one core gene absent from the main chromosome. For example, the chromid in Vibrio cholerae contains genes for the ribosomal subunits L20 and L35. While most chromids have a disproportionately smaller number of essential genes compared to the main chromosome, such as rRNA genes or the genes in the rRNA operon, some may have many more essential genes and may even be considered "equal partners" with the chromosome. In general, chromids also see an enrichment of genes involved in the processes of transport, metabolism, transcription, regulatory functions, signal transduction, and motility-related functions. Proteins located on chromids are involved in processes which can interact with proteins encoded on the main chromosome. Chromids also have more transposase genes than chromosomes, but less than megaplasmids.
Phylogenetic distribution
The presence of core genes makes the chromid essential to the survival of the bacterium. The same core genes will be found on the chromids within a genus but not necessarily between genera. All chromids of a genus may additionally share a large number of conserved but non-essential genes which help define the phenotype of the genus. In contrast, bacterial chromosomes may universally or near-universally share hundreds of conserved core genes. Plasmids contain no core genes, and unlike chromids, plasmids of different species within a bacterial genus share few genes. This is partly due to the common transfer of gain and loss of plasmids and their transfer between bacteria through conjugation, while chromids are passed on through cell divisions with no evidence of chromids moving through horizontal gene transfer. It has been observed that the chromid in at least one bacterial species could be eliminated without making the bacterium inviable, however, the bacterium did become auxotrophic indicating a severe fitness compromise associated with the loss of the chromid.Due to their stable presence within a bacterial genus, chromids also have a feature of being phylogenetically restricted to specific genera. Examples of genera of bacteria with chromids include Deinococcus, Leptospira, Cyanothece, and an enrichment of genera of the Pseudomonadota. Overall, bacterial genome sequencing indicates that roughly 10% of bacterial species have a chromid. It has also been found that there is a bias towards co-occurrence of a chromid and a megaplasmid in the same organism. Chromids also appear more frequently in phylogenies than do megaplasmids, despite megaplasmids being the putative evolutionary source for chromids. This may result in the tendency of organisms to lose their megaplasmids over time, compared with the inherently greater evolutionary stability of chromids.