The ''

Bacteroides thetaiotaomicron ''Bacteroides thetaiotaomicron'' (formerly ''Bacillus thetaiotaomicron'') is a species of bacterium of the genus ''Bacteroides''. It is a gram-negative obligate anaerobe. It is one of the most common bacteria found in human gut microbiota and is ...

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

contains hundreds of small RNAs (sRNAs), discovered through

RNA sequencing RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing c ...

. These include canonical housekeeping RNA species such as the

6S RNA In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S ...

(SsrS),

tmRNA Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with ...

(SsrA), M1 RNA (RnpB) and 4.5S RNA (Ffs) as well as several hundred

cis Cis or cis- may refer to: Places * Cis, Trentino, in Italy * In Poland: ** Cis, Świętokrzyskie Voivodeship, south-central ** Cis, Warmian-Masurian Voivodeship, north Math, science and biology * cis (mathematics) (cis(''θ'')), a trigonome ...

and

trans Trans- is a Latin prefix meaning "across", "beyond", or "on the other side of". Used alone, trans may refer to: Arts, entertainment, and media * Trans (festival), a former festival in Belfast, Northern Ireland, United Kingdom * ''Trans'' (film ...

encoded small RNAs. More than 20 candidates have been validated with northern blots and the

structures A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

of several members have been characterized through ''in silico'' analyses and chemical probing experiments. Two ''B. thetaiotaomicron'' sRNAs that have been functionally characterized are RteR and GibS. RteR is a 78

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

(nt) long sRNA that is conserved in closely related species and likely serves as a repressor of a

transposon A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transpo ...

operon In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splic ...

. Analyses based on

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

conservation, taking into consideration nucleotide covariation and in-vitro chemical probing have revealed a structure that consists of a 5’ hairpin and a Rho-independent terminator that are separated by an 8 nt sequence. GibS is a 145 nt long sRNA that is also conserved in several closely related species within phylum

Bacteroidota The phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and ...

and has been hypothesized to play a role in carbon metabolism. Structural analyses have revealed this sRNA to possess an extended 5’ single stranded region (38 nt) followed by two meta-stable hairpins and a Rho-independent terminator at the 3’ end. It is maximally expressed when ''B. thetaiotaomicron'' is grown in ''N''-acetyl-D-glucosamine as the sole carbon source and has been shown to both induce and repress target mRNAs involved in

metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...

regulation. The ''B. thetaiotaomicron'' genome also contains a large subset of

antisense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...

sRNAs that bear resemblance to the ''

B. fragilis ''Bacteroides fragilis'' is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surroun ...

'' DonS RNA. This family of 78 to 128 nt long sRNAs are encoded antisense to several of their target genes, that are members of PULs (''Polysaccharide Utilization Loci'').

References

{{Navbox , name = hide the gallery , title = Gallery of Bacteroides thetaiotaomicron sRNA , titlestyle = background:#e7dcc3 , state = autocollapse , list1 = {{Gallery , lines=5 , Image:RF04178-rscape.svg, BTnc005 Secondary structure taken from th
Rfam
database. Famil
RF04178
, Image:RF04179-rscape.svg, BTnc049 Secondary structure taken from th
Rfam
database. Famil
RF04179
, Image:RF04184-rscape.svg, BTnc060 Secondary structure taken from th
Rfam
database. Famil
RF04184
, Image:RF04177-rscape.svg, BTnc201 Secondary structure taken from th
Rfam
database. Famil
RF04177
, Image:RF04180-rscape.svg, BTnc231 Secondary structure taken from th
Rfam
database. Famil
RF04180
, Image:RF04182-rscape.svg, GibS Secondary structure taken from th
Rfam
database. Famil
RF04182
, Image:RF04181-rscape.svg, rteR Secondary structure taken from th
Rfam
database. Famil
RF04181
RNA Bacteroidia Genomics RNA sequencing Nucleic acids

See also

References